The station, along with the rest of the line was acquired by the Flushing and North Side Rail Road in 1869.

A railway express elevator building was then opened on the eastbound side until the Port Washington Branch stopped carrying freight.

The 1928 express/baggage station remains today, being converted into a local community center.

During the 2005 New York City transit strike, Bayside was one of the few stations that Port Washington trains stopped at, and lesser-used stations such as Auburndale and Murray Hill were bypassed.

[5][6] The station has two slightly offset side platforms, each 10 cars long.