During the 1920s and 1930s, the vicinity of the station became the site of numerous horrific accidents involving crashes with trains at the unguarded grade-level rail crossings at Straight Path, 18th Street and Little East Neck Road.

The miniature railway moved to Freeport in 1953, when the LIRR needed the land on which the New York Live Steamer Society had been using without charge.

It was replaced with a non-descript, flat-roofed, 37' x 12', $40,000 concrete block depot on the north side of Long Island Avenue about 500 feet (150 m) west of the 1875 station.

These upper middle class commuters boarded at Wyandanch since it was closer than the LIRR depot in Huntington Station.

As part of an attempt to speed commuting times through Suffolk County, they wanted to eliminate railroad service in Wyandanch after 108 years.

Working on a bipartisan basis, Senator Owen Johnson (R-West Babylon) and Assemblyman Patrick Halpin (D-Lindenhurst) convinced the MTA to maintain rail service in Wyandanch as well as Pinelawn.

On July 13, 2013, the LIRR and state and local elected officials broke ground on "Wyandanch Rising," a 40-acre transit-oriented development project that is to create an intermodal facility at the station, including a parking facility for 900 cars and a new station building; an apartment and retail complex is under construction.