If you meant to update those products, run the import again and tick "Update existing products". If they are different products, give each one its own SKU. Variations need their own SKU too, different from the parent's. The checker lists every SKU repeated inside your file; it cannot see the SKUs already in your store.

WooCommerce import error: "A product with this SKU already exists."

What it means: On a normal import (new products), WooCommerce skips any row whose SKU is already used by a product in your store. It also happens inside one file: the first row with a SKU creates the product, and every later row with the same SKU is skipped. The import finishes with these rows listed as skipped.

Find the rows in your file

WooCommerce product import

Choose file

The product CSV you are about to import into WooCommerce (Products, Import), or the one that just failed.

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How to fix it

If you meant to update those products, run the import again and tick "Update existing products".
If they are different products, give each one its own SKU. Variations need their own SKU too, different from the parent's.
The checker lists every SKU repeated inside your file; it cannot see the SKUs already in your store.

Example

A file with this problem

Type,SKU,Name,Published,Visibility in catalog,Tax status,In stock?,Stock,Regular price,Images,Parent,Attribute 1 name,Attribute 1 value(s...
simple,MUG-1,Mug,1,visible,taxable,1,5,12.00,,,,,
simple,MUG-1,Large Mug,1,visible,taxable,1,5,15.00,,,,,

What the checker says about it

Line 3: SKU "MUG-1" is also on line 2. On a new-products import the first row creates the product and this row is skipped with "A product with this SKU already exists."; with "Update existing products" ticked, this row overwrites what line 2 imported instead. Give every product and variation its own SKU.

Once the listed rows are fixed, check the file again; the checker also looks for the other problems in WooCommerce's import code, so you do not trade one error for the next.

Other WooCommerce import errors

Sources

WooCommerce 11.2.2 source: class-wc-product-csv-importer.php: https://github.com/woocommerce/woocommerce/blob/11.2.2/plugins/woocommerce/includes/import/class-wc-product-csv-importer.php
WooCommerce: Product CSV Importer and Exporter: https://woocommerce.com/document/product-csv-importer-exporter/

Based on WooCommerce 11.2.2's import code and documentation. Not tested on a live store.