[4] Subsequently, the branch is one of the Long Island Rail Road lines most vulnerable to closure, and it was threatened with abandonment in the past.

On January 26, 1892, the New York Bay Extension Railroad Company was incorporated as a subsidiary of the Long Island Rail Road to build a line running from Garden City to a point in the town of New Lots in Kings County near the intersection with the New York, Brooklyn & Manhattan Beach Railway Company.

[13] The LIRR leased its property in 1897, and formally merged with the New York Bay Extension Railroad on August 29, 1902.

The upper end of the branch was electrified in 1911 or 1912 from Country Life Press to Franklin Avenue in Garden City to allow MU baggage cars access to the Doubleday plant.

[5] On October 19, 1926, the portion of the line between Valley Stream and Franklin Avenue in Garden City was electrified at the cost of $1 million and it was inaugurated with a special train.

The connection to the Oyster Bay Branch was severed in 1928, while the portions of the line between Mineola and Country Life Press and between Country Life Press and West Hempstead were taken out of revenue passenger service on September 15, 1935 due to the costly grade crossing elimination improvements imposed upon the LIRR by the Interstate Commerce Commission, as well as the New York Public Service Commission.

Following the full opening of Grand Central Madison, service to Atlantic Terminal in Brooklyn was cut back to a shuttle to Jamaica.

To compensate for the lack of through service to Brooklyn and to allow for cross-platform-transfers at Jamaica for Brooklyn-bound customers, off-peak West Hempstead trains stopped serving Valley Stream and began running hourly through to Atlantic Terminal with peak trains now serving both Penn Station and Grand Central Terminal as of February 27th, 2023.