[3] Construction began in June 1866,[4] and it opened for regular service from Jamaica east to Babylon on October 28, 1867.

[6] The SSRRLI was forced to build its own line west of Jamaica due to the LIRR's purchase of the New York and Flushing Railroad on July 13, 1867.

The South Side had been looking at using the New York and Flushing Railroad for access to Long Island City.

To gain access to ferry service to New York City, the South Side decided to build to Williamsburg.

[10] The South Side thus gained a new freight terminal at Long Island City by rebuilding part of the old New York and Flushing, but passenger service continued to operate to Williamsburg.

[2] Prior to the acquisition by the LIRR, there was a proposal by the SSRRLI to extend the main line southeast towards Bellport, and then northeast to Brookhaven and Southaven.

While constructing it in summer 1869, the company installed about 700 feet (200 m) of tracks across William B. McManus's farmland near Lawrence.

[15] The South Side entered receivership on November 9, 1873,[15] and was sold on September 16, 1874 to the Poppenhusens, who also controlled the Flushing, North Shore and Central Railroad.

The two Poppenhusen lines were connected at Babylon, and the Southern's branch to Hempstead was abandoned temporarily after only two years of operation.