Brooklyn's banning of steam locomotion caused the tracks to be taken over by horse car lines until 1877. Brooklyn, Flatbush, and Coney Island Railroad's rapid transit trains began stopping at Atlantic Avenue and it soon began developing again. In 1882, the Long Island Express Company moved in and installed the tracks that would give Atlantic Yards its name. Additionally, the Union Elevated Railroad would build an elevated line at the same spot. Atlantic Station had become a major transit hub.

Work on the Vanderbilt Avenue Freightyards began in 1904, marking a new era for the station. Improving and replacing the Carlton Freight Yards, the Vanderbilt Yards prompted a full renovation of the depot that amounted to a reconstruction of the station.

The new terminal had subway like entrances that lead to the tracks (which had been moved underground.) Its lobby was spacious and expansive to provide an aesthetic meeting place for those arriving and departing. Different sections and spaces were designed for freight, produce, and merchandise entering the station.

The BMT and IRTC added Subway Lines (three in total) that stopped at the new Atlantic Station. These lines linked the busy new terminal to the rest of the city and secured Atlantic Station's role as a premier rail transit hub in Brooklyn.

As rail declined, the city allowed a plethora of businesses to set up shop in Atlantic Terminal. Soon (as pictured here), lunch counters, flower shops, dry cleaners, and bars populated the interior of the terminal. The station began slipping into disrepair and as wear and tear intensified, parts of the station were even razed.

However, in 2010, the Atlantic Terminal received a much-needed renovation to its main entrance. After years of neglect, it has returned to its prominent place in Brooklyn rail travel.