It was built in 1873 as part of the Babylon Extension of the Central Railroad of Long Island (CRRLI), which was owned by Alexander Turney Stewart.

The branch was mostly unused following the 1876 merger of the CRRLI and the LIRR, but in 1925 it was rebuilt and reconfigured to connect Bethpage and Babylon stations.

This allows non-electric Montauk Branch trains that begin or end east of Babylon to use the Main Line from Bethpage to Jamaica.

It was along this stretch of the Central Branch that Mile-a-Minute Murphy set a record in 1899, pedalling a bicycle for one mile behind a train in less than one minute.

This will alleviate service disruptions by allowing electric trains to travel between the Ronkonkoma and Babylon Branches, which are both electrified.

The portion of the line from Garden City to just west of the disconnection at Bethpage Junction were called the Central Extension.