Days ahead of its planned breakup, eBay Inc. suffered a blow in its effort to sell its eBay Enterprise unit as one of the division's biggest customers said it would move much of its business elsewhere.

Toys "R" Us Inc. on Thursday said it would take control of its own U.S. e-commerce operations by mid-2016, rather than relying on eBay Enterprise. The announcement comes at an inopportune time for eBay, which has been in talks with Thomas H. Lee Partners LP to sell the unit for as much as $1 billion, according to people familiar with the matter.

The e-commerce company has been searching for a buyer since at least January, when it said it could also seek a spinoff of the division. In recent weeks, Thomas H. Lee had outbid other potential suitors including a grouping of private-equity firms, Apax Partners and Sterling Partners, people familiar with the matter said.

Even before the Toys "R" Us announcement, talks between eBay and Thomas H. Lee had reached a standstill over price. The two sides have discussed a price range of between $800 million and $1 billion, two of the people said. That price would be less than half the $2.4 billion that eBay paid in 2011 for the unit, then known as GSI Commerce.

In the hopes of securing a deal, eBay had extended the prior deadline of June 30 to July 15, which is two days before eBay's planned split from its PayPal payments unit, according to one of the people.

There is no guarantee a deal will be reached by then, some of the people cautioned. Reuters reported earlier that talks continued between eBay and Thomas H. Lee.

EBay Enterprise helps power the online retail sites for companies such as IKEA and the National Basketball Association. The division took in $1.24 billion in revenue last year, a 6% increase from the prior year, representing about 7% of eBay's $17.9 billion in sales.

Toys "R" Us, based in Wayne, N.J., said bringing much of its e-commerce operations in-house would provide it an improved customer experience. The retailer has been a customer of eBay Enterprise since 2006, and will continue to use its services in Europe and Canada.

When eBay bought GSI it had had sales of $1.36 billion in 2010, which then included retail sites Rue La La, ShopRunner and Fanatics. Those three companies are now owned by a separate holding company called Kynetic LLC.

In early 2014, eBay Enterprise lost its president, Chris Saridakis, who was subsequently sentenced to 15 months in prison on insider-trading charges related to the sale of GSI Commerce. Craig Hayman, a former International Business Machines Inc. executive, now runs the division.

EBay is unloading Enterprise as part of its plan to focus on its core marketplace. The San Jose, Calif., company is spinning off PayPal on July 17, making two publicly traded companies.

EBay has been cleaning up other loose ends before its new life as a stand-alone company. In June, it sold back to Craigslist Inc. 28.4% it had held in the classified-ad site since 2004 for an undisclosed amount, while also settling remaining litigation.

Earlier this year, eBay pared about 2,400 jobs, representing roughly 7% of its workforce. Longtime Chief Executive John Donahoe, who had vigorously fought investor Carl Icahn's initial proposal for the breakup, is stepping down and will become chairman of PayPal.

For Thomas H. Lee a deal would give the firm a foothold in e-commerce, adding to its wide portfolio, which includes MoneyGram International Inc., Spanish language broadcaster Univision Communications Inc. and 1-800 Contacts Inc.

The Boston firm, which took retailer Party City Holdco Inc. public in April, focuses on making investments in three sectors: business and financial services, consumer and health care, and media and information services.

Write to Greg Bensinger at greg.bensinger@wsj.com and Gillian Tan at gillian.tan@wsj.com

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