Bostancı station was originally built by the Ottoman government, as part of a railway from Kadıköy to İzmit, and was opened on 22 September 1872.

In 1909, the CFOA began frequent train service from Haydarpaşa and Pendik, stopping at Bostancı station, which was expanded and rebuilt in 1910.

Many houses with large gardens were built around the station for Constantinople's wealthy residents, who used the train service to commute into the city.

The station was electrified in 1969 with overhead wire, when TCDD began operating electric commuter rail service.

Bus service can be accessed via two stops, one on Bağdat Avenue and one on Çetin Emeç Boulevard, on the waterfront.

A 14.2 km (8.8 mi) long metro line to Dudullu connects to Bostancı station.