The toy giant's warehouse style store at Lakeside will shut its doors next year as one of 26 across the UK.
The firm's other branch in the Frenchgate Centre remains unaffected.
The retailer confirmed that it is set to close a quarter of its UK shops after announcing that its warehouse style stores are too expensive to run.
There are currently 106 branches of Toys R Us in the UK and the retail giant plans to close at least 26 of them.
Speculation of the future of the company's future in the UK has been circulating since September when the retailer filed for bankruptcy in the US and Canada.
Now, the firm plans to use a Company Voluntary Arrangement (CVA), which will allow the retailer to pay off its debts over a fixed amount of time.
Steve Knights, managing director of Toys R Us UK, said: "Like many UK retailers in today’s market environment, we need to transform our business so that we have a platform that can better meet customers’ evolving needs.
"The decision to propose this CVA was a difficult one, but we determined it is the best path forward to make essential changes to the business."
All of the earmarked stores will remain open over Christmas and into the New Year. The Doncaster branch is scheduled to close by next spring.
Toys R Us has said that they will continue to honour gift cards and Take Time To Pay agreements and there will be no change to the returns policy.
It plans to turn existing locations into smaller interactive stores as well as relaunching the website.