Kazlıçeşme station was opened on 4 December 1955 by the Turkish State Railways as a stop on the Istanbul suburban line.

The new station had the same platform design, but added a third track for passing intercity and regional trains.

Seven months later, on 29 October 2013, the new Kazlıeşme station opened as the western terminus of Marmaray trains from Ayrılıkçeşmesi in Kadıköy.

However, due to contractor issues, phase II of the Marmaray project was delayed, effectively cutting off Kazlıçeşme from the rest of the national rail network for a few years until work restarted in mid-2016.

Once phase II completed on March 12, 2019, Kazlıçeşme is a stop on the Halkalı to Gebze commuter rail line.