Hoyt Street is the northernmost four-track station on this line. It is located under the intersection of Fulton Street, Hoyt Street, and Bridge Street. It has two side platforms serving only the local tracks. Trains from the Clark Street Tunnel run on the local tracks and those from the Joralemon Street Tunnel run on the express tracks. The original construction included only the Joralemon Street Tunnel with crossover switches north of Hoyt Street. These switches have been removed and new ones were installed between Nevins Street and Atlantic Avenue, so trains from the Joralemon Street Tunnel cannot stop at this station at all.
Southbound (east Brooklyn-bound) trains use track E1 while northbound (Manhattan-bound) trains use track E4. Southbound and northbound express trains use tracks E2 and E3, respectively. Track numbers and letters are used for chaining purposes and are rarely, if ever, used by passengers.
The station has been extensively renovated; old signs reading "Hoyt Street – Bridge Street" remain on the I-beams separating the local and express tracks. At the north end of the southbound platform is a closed crossunder that included an entrance to Macy's; the south end of the northbound platform includes a passageway that is used by police. One of the original ceramiccartouches from the station is now on display at the New York Transit Museum.
Stations and line segments in italics are closed or demolished. Track connections to other lines' terminals are displayed in brackets. Struck through passenger track connections are closed or unused in regular service.