Homebase announced in February it was to shut 40 of its stores across the United Kingdom - more than a sixth of its 250 stores - but did not disclose which ones were to close.
City of York Council leader Ian Gillies said: "It is obviously a blow to York's retail offer.
"York is not the only one. It mirrors the closure of other Homebase stores nationally. However, we in York must work to attract other retail outlets to mitigate its loss."
UK retailers are struggling in the face of Internet competition, rising inflation and fragile consumer confidence.
In York, shops to close in recent times include BHS and River Island, with Dorothy Perkins/Burtons in Coney Street at risk.