That same summer local Atlantic Avenue rapid transit trains began to stop there on August 13.

The headquarters for the Long Island Express Company was installed there in 1882, and gave the station a series of tracks that would later be known as the "EX Yard."

The decline of rail service after World War II led to the station's gradual demise, however.

Despite efforts to repaint the lobby in the early-1980s, random vandalism plagued the station interior causing water damage that was so severe, the street level depot was closed in 1988,[8] and portions were razed during the 1990s.

[10] On January 5, 2010, a new entry pavilion, designed by di Domenico + Partners, opened, providing improved connections between the LIRR, subways, and buses.

[11] In March 2010, the station was renamed Atlantic Terminal after a six-year reconstruction project,[12] during which trains continued to operate.

In 2014, the LIRR announced that service from Babylon and Hicksville would go directly to Atlantic Terminal during New York Islanders games at Barclays Center.

[14] During the morning rush hour of January 4, 2017, a train overran the bumper block at the end of track 6, injuring 103, none seriously.

[17] The accident occurred at about 8:20 a.m. Two cars of the six-car M7 electric multiple unit train involved were severely damaged when it collided with the bumper at a speed of 10 to 15 miles per hour (16 to 24 km/h).

[15] The National Transportation Safety Board (NTSB) and Federal Railway Administration opened investigations into the accident.

The massive Pacific Park residential, commercial and sports complex, which includes Barclays Center, is being built near the station and above its yard tracks.