Setting up Shopify shipping is easier when you decide more than the standard charge. You also need to decide the purchase amount for free shipping, any regional differences, and what happens when a customer buys a product that ships separately.
For example, a store might charge ¥870 for standard shipping and make it free on orders of ¥7,700 or more. If Okinawa is excluded from free shipping and a separately shipped product has a ¥500 charge, those conditions also belong in the settings and customer guidance. Making standard shipping free does not necessarily remove the separate shipping charge.
This article uses that rate table to show what to enter in the admin and what amounts to check at checkout. It covers ordinary retail orders shipped within Japan. Set up the basic rate first, then add the regional and separate-shipment settings only if your store needs them.
Build a shipping rate table for your store
Decide what your store can cover
Start with the carrier charge for packing commonly ordered products into one parcel. Add the cost of the box, cushioning materials, and fulfillment work. Use your own costs from your carrier contract or warehouse invoices. Separate out destinations or large products that cost more to ship.
If you charge the customer less than those costs, your store covers the difference. For a free shipping order, your store covers all delivery costs. When choosing a free shipping threshold, subtract product costs and payment fees from an order at that amount, then see whether enough remains to cover delivery and leave the profit you need.
Suppose shipping a single order costs ¥800 in carrier charges, ¥100 in packaging materials, and ¥200 in fulfillment work. All the amounts below are fictional examples for explanation. They are neither typical carrier prices nor actual contract rates.
| Calculation | Example |
|---|---|
| Delivery cost for one order | ¥800 + ¥100 + ¥200 = ¥1,100 |
| Cost covered by the store when it charges ¥870 for shipping | ¥1,100 − ¥870 = ¥230 |
| Amount left on a ¥7,700 product order with free shipping | Assuming ¥4,200 in product costs and ¥300 in payment fees: ¥7,700 − ¥4,200 − ¥300 − ¥1,100 = ¥2,100 |
The ¥2,100 comes before advertising and fixed costs. If a store needs to retain ¥2,400 to pay those costs and leave a profit, this example falls short by ¥300. Reconsider the free shipping minimum and run the same calculation for an order at the revised amount. If covering ¥230 on an order that pays shipping is too much, reconsider the standard rate too. Replace all these figures, including the amount you want to retain, with your own before adopting the conditions.
Record these four decisions in your shipping rate table:
| Decision | Example entry |
|---|---|
| Shipping for standard products | ¥870 outside Okinawa |
| Free shipping condition | Standard shipping for standard products is free when the order's product amount is at least ¥7,700 |
| Regional difference | ¥1,200 to Okinawa, with no purchase-based free shipping |
| Separately shipped products | ¥500 within Japan; add this charge to the standard product's shipping charge when the two are purchased together |
The ¥870 rate and ¥7,700 threshold are examples used in the steps below. Choose amounts that suit your store and substitute them. If every product can ship under the same rate, you do not need the separate-shipment row.
Separate products from destinations
A Shopify shipping profile groups products that use the same shipping rules. Use the general shipping profile for standard products. Create another profile for products, such as large items, that need a different rate.
A shipping zone groups destinations. If Tokyo and Okinawa need different charges, separate those destinations within the same profile. Use shipping zones for regional differences and shipping profiles for product differences to choose the right place to configure each rule.
Find the shipping settings
In the Shopify admin, open Settings → Shipping and delivery. If you see the general shipping profile and a product list, with shipping zones and rates inside the profile, you can follow the steps below.
Shopify is also moving shipping settings into Markets in stages. If Shipping and delivery shows a market-based view with Shipping options, open Markets → a market that includes Japan → Shipping. Set the ¥870 flat rate and ¥7,700 free shipping minimum in that shipping option. Follow the official instructions for the Markets approach instead of mixing it with the shipping-profile steps below. Rates are also combined differently when products are mixed.
Set standard shipping to ¥870, free from ¥7,700
Enter the standard shipping rate
From Shipping and delivery, open the general shipping profile and select the zone that includes Japan. If Standard shipping already exists, use its … menu to open Edit shipping option. To add it, choose Add shipping option and enter these values:
| Field | Value to enter or select |
|---|---|
| Name | Standard shipping |
| Rate type | Flat rate |
| Rate | ¥870 |
| Offer free shipping | On |
| Minimum order amount | ¥7,700 |
The name appears at checkout. Choose a name customers can understand when selecting a method, such as “Standard shipping” or “Refrigerated shipping.” If you display transit times, choose a number of days that matches your carrier or warehouse arrangements.
After entering the values, select Done, then Save on the profile page. Return to the list and check that “Standard shipping ¥870” and the “free from ¥7,700” condition are still there. Closing the edit panel with Done alone does not finish saving the profile.
If your store charges ¥870 regardless of order value, leave free shipping off and save. The free shipping configured here is a shipping rate customers can select when the condition is met. They do not need to enter a discount code.
Check the free shipping threshold at checkout
Add a standard product to the cart from your storefront and proceed to checkout. Enter a destination, then look at Standard shipping under shipping methods and the Shipping amount in the order summary. Start without a discount code so you can trace the condition you configured.
At the same Tokyo destination, checkout showed the following for carts containing only standard products:
| Product subtotal | Standard shipping | Displayed total |
|---|---|---|
| ¥6,000 | ¥870 | ¥6,870 |
| ¥7,700 | Free | ¥7,700 |
The ¥7,700 cart contained one product each at ¥6,000, ¥750, and ¥950. All three belong to the general shipping profile. Adding a product with a different shipping rule just to reach the threshold introduces the combined-rate behavior described later. Test with products under the same shipping rule first.
If shipping is not free, reopen Standard shipping in the general shipping profile. Check that the free shipping minimum is ¥7,700 and that you saved the changes. If another method, such as express shipping, is selected, switch to standard shipping. The free shipping condition applies to the method where you set it.
If your store accepts discounted orders, test again with a coupon you normally use. Shopify assesses price-based conditions using the cart amount after discounts and before tax. For example, an eligible amount of ¥8,000 falls to ¥7,200 after a 10% discount, below the ¥7,700 threshold. The amount payable also includes shipping and other charges, so a displayed total of ¥7,700 or more does not by itself mean shipping is free.
Set the Okinawa rate to ¥1,200
For a region with a different rate, create a separate shipping zone in the general shipping profile. This example divides Japan into “¥870 outside Okinawa, free from ¥7,700” and “¥1,200 in Okinawa, with no free shipping condition.”
- In the general shipping profile, use the … menu to edit the zone that contains Japan.
- Expand Japan's prefecture list and deselect Okinawa Prefecture. Name the zone “Domestic shipping (excluding Okinawa Prefecture),” select Done, and then Save on the profile page.
- After saving, select Add zone, name it “Okinawa Prefecture,” and select only Okinawa Prefecture in Japan. Select Done to create the zone.
- Add Standard shipping (Okinawa Prefecture) to the Okinawa zone. Choose Flat rate, enter ¥1,200, and turn Offer free shipping off.
- Select Done, then Save for the whole profile.
Within the same profile and shipping-origin group, a region cannot belong to two shipping zones at once. If you cannot select Okinawa Prefecture for the new zone, check whether you removed it from the original Japan zone and saved the profile. Selecting Done alone may not make it available for the new zone. Afterward, check that both the “excluding Okinawa” and Okinawa zones still have a shipping rate.
Once saved, use the same ¥6,000 product and change only the checkout destination from Tokyo to Okinawa. With these settings, checkout showed ¥870 shipping to Tokyo and ¥1,200 to Okinawa. The respective totals on a ¥6,000 product subtotal were ¥6,870 and ¥7,200. If you change products or quantities as well, it becomes harder to tell whether the destination or order amount caused the difference.
If checkout still charges ¥870 for Okinawa, recheck the prefecture and postal code entered at checkout and whether the Okinawa rate was saved in the general shipping profile. If checkout says delivery to Okinawa is unavailable, check whether you forgot to add a rate to its zone. After correcting the setting, reopen checkout with the same product, quantity, and Okinawa address.
Charge ¥500 for a separately shipped product
Assign the product to another shipping profile
Move a product to a custom shipping profile if you want to charge for its shipping separately even when it is ordered with a standard product. This applies to products such as large items, refrigerated goods, or goods shipped directly from a supplier when their actual shipping arrangement and intended charge differ.
- Open Settings → Shipping and delivery, then Add custom profile.
- Give it an admin name such as “Separately shipped products,” and choose the relevant products and variants under Products.
- Check that the shipping origin is a location that actually ships those products.
- Create a shipping zone that includes Japan, then add Separate shipping as a shipping option. Choose Flat rate, set it to ¥500, and leave out a free shipping condition.
- Select Done, then Save the profile.
If the relevant products already have a profile, edit its product list and rates. A product or variant can belong to only one profile. Adding it to a different profile removes it from the original one, so check the names you selected rather than moving standard products as a group.
In the image, “Popaz Lab 配送プロファイル検証用” is the separately shipped product. It is assigned to “記事検証用・別配送プロファイル,” with a ¥500 rate for the method labeled “別配送テスト.” That label is the test-store equivalent of “Separate shipping” in this article's example.
Check the amount when both product types are purchased
After checking standard products and separately shipped products on their own, add both types to one cart. In an example shipped to Tokyo with one ¥6,000 standard product and one ¥1,000 separately shipped product, the product subtotal was ¥7,000, shipping was ¥1,370, and the total was ¥8,370.
The ¥1,370 shipping charge consists of ¥870 for standard shipping and ¥500 for separate shipping. The two products use different shipping profiles, and their charges are added together. If checkout says the order will arrive in two packages, also look at the method and charge for each package.
The flat ¥500 rate does not add another ¥500 every time you increase the quantity of a product in this profile. If you need to charge per item, consider another way to collect that amount instead of using this flat rate table unchanged.
Read the free shipping threshold and separate charge together
Even when standard shipping is free, the separate ¥500 charge is calculated on its own. The purchase amount condition uses the amount for the whole cart, not just the subtotal of standard products.
For example, a Tokyo order with a ¥6,000 standard product and two ¥1,000 separately shipped products has an ¥8,000 product subtotal. At checkout, standard shipping was free and the separate ¥500 charge remained. Total shipping was ¥500 and the amount payable was ¥8,500. Although standard products still accounted for only ¥6,000, the whole cart met the ¥7,700 condition.
The “別配送テスト” label in the image is the ¥500 shipping method for the separately shipped product.
Telling customers that they must buy at least ¥7,700 of standard products for free shipping would conflict with this setting. Telling them that all shipping is free on orders of ¥7,700 or more would leave out the separate ¥500 charge. Explain both the condition for free standard shipping and the charge for separately shipped products.
If you intend to charge for shipping only once even when different products are purchased together, consider whether the products can use the same shipping rule before creating more profiles. Do not group products with different shipping origins merely for the sake of the settings; decide with your warehouse or fulfillment team based on how they will actually ship.
Correct an unexpected shipping charge
When the shipping amount is unexpected, note the products, quantities, destination, and any discount used, then check the relevant setting below. Change one condition at a time. After correcting it, reopen checkout with the same conditions.
| What happens at checkout | Where to look and what to correct |
|---|---|
| Standard shipping is charged on an order that should qualify for free shipping | Open standard shipping in the general shipping profile and correct the free shipping minimum. Also check the amount after discount and the selected method at checkout. |
| Okinawa has the same charge as the standard region | Open the Okinawa zone in the general shipping profile and correct its eligible region and ¥1,200 rate. Save the profile afterward. |
| Shipping increases as soon as a separately shipped product is added | Check the profiles of both products. If ¥870 plus ¥500 is the intended result, explain the breakdown to customers instead of lowering the charge. |
| A high-value order says it cannot be shipped | If you use price-based rate ranges, leave the Maximum for the highest range blank. Check for gaps between ranges too. |
| Only one product says it cannot be shipped | Open that product's profile and check the shipping origin and destination zone. Add a rate to the relevant zone. |
| A saved rate does not appear at checkout | Read the saved value again in the admin. Start a new checkout from the storefront cart instead of reusing an old abandoned checkout. |
Check the outcome you expected from each correction. If you changed the Okinawa rate, check for ¥1,200 with the same ¥6,000 product and Okinawa address. If you removed the upper limit on a rate range, check that the high-value cart can select a shipping method again.
Make your shipping information match the settings
For this rate table, your shipping information could read as follows. Replace the amounts and eligible products with conditions you have checked through checkout in your own store.
Shipping for standard products is ¥870, except to Okinawa Prefecture. If your order's product amount is ¥7,700 or more, standard shipping for standard products is free. Shipping to Okinawa Prefecture is ¥1,200 and does not qualify for purchase-based free shipping.
Products marked “Separately shipped” incur an additional ¥500 shipping charge. If you order them with standard products, the applicable charges are added together. The separate ¥500 charge still applies when standard shipping is free.
The free shipping condition is assessed using the product amount after discounts. Please check the shipping charge at checkout before placing your order.
Mark eligible products on their product pages so customers know before buying which ones ship separately. If you also set a rate for express shipping, explain it separately from the standard shipping condition above.
Before publishing shipping information, fill in the checkout results your store needs in this table:
| Products and destination | Expected shipping | Shipping at checkout |
|---|---|---|
| Standard products, below the free shipping threshold, standard region | ¥870 | Fill in |
| Standard products, exactly at the free shipping threshold, standard region | ¥0 | Fill in |
| The same standard products, Okinawa | ¥1,200 | Fill in |
| Standard and separately shipped products, below the threshold, standard region | ¥1,370 | Fill in |
| Standard and separately shipped products, at or above the threshold, standard region | ¥500 | Fill in |
If your store uses regular coupons, add cases with those codes entered. Once the expected and actual shipping charges match, you can give consistent conditions in the shipping rate table, product pages, and banners.
If you are unsure how to set up shipping for your store, contact Popaz. Tell us about your products and shipping arrangements, and we can work through the configuration approach together.
References
Information about features and settings is current as of October 2026.
