Known for its iconic yellow awning, the 501 Bloor Street West location was a flagship store for the family-owned mini-chain, opened in 1976.
"Our Annex location is closing this spring. Stop by soon for amazing deals," wrote BookCity on its Twitter account.
BookCity's other three other locations, including at Yonge Street and St. Clair Avenue, on Danforth Avenue and on Queen Street East, will continue to be open for business.
In 2012, a BookCity location in the High Park neighbourhood was also shut down.