The trackage of the Garden City–Mitchell Field Secondary, originated in the 1870s as part of the Central Railroad of Long Island (CRRLI).

The rest of the Central between Garden City and Bethpage saw much use during the early part of the 20th century, but with the advent of the automobile in the 1910s, followed by the Great Depression, the 1930s saw this portion of the line dwindle in service.

[1][4][5] The only bright spot for the line came when Mitchel Field, an air force base, opened during World War I in the expansive area of the Hempstead Plains.

Some of the trackage was relaid so as to provide the materials needed in the Levitt construction, and for a while, a small passenger shuttle was instituted by the LIRR between Garden City and Plainedge.

[1][4][5] A large freight yard remained in Garden City, servicing some local industries such as A&P, General Bronze, and Newsday.

However, lack of resources (at the time the bankrupt LIRR was in the process of being bought by the MTA from the Pennsylvania Railroad), as well as community opposition from residents in Garden City shelved those plans.

In the 1980s through late 1991, the LIRR had several customers on the line, or in the team yard, who were switched once or more a week: White Rose, at the end of the spur that ran northeast out of the yard, at Zeckendorf Boulevard, a plastics customer at the end of the line at Endo Boulevard, at one of the entrances to Nassau Community College, the waste ash from the Town of Hempstead's incinerator next to the Meadowbrook State Parkway, and off-line customers who received boxcars, flatcars, and gondolas of various types of goods in the team yard by Stewart Avenue.

As the years went on the remaining freight customers along the line also disappeared as the LIRR focused its resources on passenger service and constructing the East Side Access project, linking from Long Island to New York City's Grand Central Terminal via Grand Central Madison.

[4][5] The Long Island Rail Road formally transferred freight operations to the New York and Atlantic Railway in May 1997.

The Clinton Road passenger station, from the line's early days, still stands along with its low level concrete platforms.