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Coney Island-Stillwell Avenue is a brand new modern train terminal for all four BMT Brooklyn Subway Lines that come together to terminate at the station. The station is located at a viaduct and its large, modern train shed (the stop was closed for all service except West End Line trains from 2002 to 2004, with the Sea Beach Line returning in 2005) that is completely new and is now a huge landmark of Coney Island. The train shed is a towering structure that is reminiscent of those still found all over Europe. The panels that protect passengers from the elements beneath it are photovoltaic cells that provide a bit of the electricity needed to power the station. The shed covers about two-thirds of the length of the station platforms, with the most northern couple cars of trains exposed to the elements. Even through the station is a terminal it is by far not-stub end, six-of the eight tracks continue all the way through the terminal.

The station has four island platforms for it's eight tracks. Each branch has a single platform and two tracks for its terminating operation. Even through the station is the southern terminal of all four-subway lines it serves it is actually located on a north-south axis. West End (D) and Sea Beach (N) Line trains approach the terminal from its northern end, and their pairs of terminating tracks become the two outside platforms at the terminal. The West End terminal tracks are the only stub-ended tracks, on the western side of the superstructure. The Sea Beach Line tracks continue south of the station and join-up with the Brighton Line's south of the station. The middle two platforms and four tracks are used by Culver and Brighton Line trains. The Culver line's platform (and the West End's that it's next to), is at a slightly lower level than the Brighton and Sea Beach Line platforms, both of these tracks switch onto the Sea Beach and West End Line tracks north of the station, making them also through tracks.

For transfers at the northern end of trainshed and still beneath it there is a bridge that connects all four platforms with stairs and has elevator access up from the Sea Beach and West End Platforms, this pair of elevators providing the only access to West End Line (D) trains. From this bridge there is a building above the tracks that has rooms for various non-public such as crew quarters.

The station's main exits are towards the southern end of the station's platforms, and are in a large concourse that is maybe a half story above street level. From the Sea Beach, Culver and Brighton Line platforms there is a gradual ADA ramp, as well as a more staircase down from each platform to this main area. The West End Line is accessed from the central exit concourse from its own passageway with some stairs that go up a bit high before reaching its own staircase and non-ADA ramp up to its platform. To exit the station there are two fare control areas, one leads north and out to the full-time bank of turnstiles and down some steps (an ADA ramp is provided), to the station's bus bay located beneath the station. This bus bay is right across from where Mermaid Avenue ends in a T-junction at Stillwell Avenue. The more mainstream exit for beach goers is through a couple of large banks of turnstiles (and a couple of High Entrance Turnstiles, for use during the dead of night between 12:45am and 6:30am, when the token booth here is closed), and a series of staircases and an ADA ramp lead down to ground level where their is a large concourse that is complete with a shopping arcade (some have storefront access, others only are accessed from the subway), as well an NYPD transit police station. There are massively wide entrances but the station doesn't have any doors anywhere out to the eastern side of Stillwell Avenue, a bit south of the busway, and the grand station entrance (that is a walk down the shopping arcade to reach the subway) at Serf Avenue, almost at its NE corner with Stillwell Avenue. The facade of this main station building has been decorated with various features that are trying to replicate the old BMT terminal. This is completed with some detailed work of red BMT Lines text on a green tiled background. The entire station still feels really new, but has a retro feel that tries to bring back features of old grand train stations such as a high train shed and replica facade from the old station. All in all the new Coney Island terminal provides an excellent greeting structure for amusement and beachgoers to an old New York City Attraction that was established by the extension of originally elevated lines that became subway lines over a hundred years ago.