The route that is the current B Train began as the West End Line, a mid 19th century tourist railway through Southern Brooklyn, called the 'West End Line,' that took holiday makers to the resort at Coney Island. This is the portion of the current B route from approximately Fort Hamilton Parkway to Coney Island.

Eventually, the West End Line was acquired, along with the rest of the South Brooklyn railways, by the Brooklyn Raid Transit Corporation, or BRT, later the Brooklyn Manhattan Transit corporation, or BMT. The BMT operated the vast elevated transit network in Brooklyn at the turn of the century, and was one of the two private companies, along with the Interboro Rapid Transit, that built the initial portions of the New York City subway and whose systems, along with the city built Independent, were consolidated to form the subway system as we know it.

The BMT initially tied the West End line into the rest of its network through the Fifth Avenue Elevated, which led south from Downtown Brooklyn through Park Slope to the southern end of Greenwood Cemetery. The Fifth Avenue Elevated was tied into the rest of the BMT network, which included tracks over the Brooklyn Bridge. The ramps that led from the trench of the West End line's extension up to the elevated tracks are still there and visible today, at the point where the B route crosses Fifth Avenue.

By 1920 the BMT had already completed one subway route between south Brooklyn and Manhattan, the line that runs up Brooklyn's Fourth Avenue, across the East River on one of two routes, and up Broadway (today's R Train). The West End line was extended to Fourth Avenue and connected into this line for through service. Trains could run either through the Montague Street tunnel to the Broadway line in the financial district, or over the north side Manhattan Bridge tracks to Canal Street, where they joined it. The two Manhattan access lines, via the bridge and via the tunnel, diverged at De Kalb Avenue.

In the late 20s and early 30s, the city built its own Independent system to compete with the BMT and IRT. The Independent, or IND, included the rest of the route of today's B, a trunk line under Sixth Avenue in Manhattan connecting to a line under Central Park West and the Concourse Line under the Grand Concourse in the Bronx. The express tracks under Sixth Avenue were not yet built and the line was not yet connected to the Manhattan Bridge.

In 1940 the city consolidated the three formerly separate transit systems and began the task of unifying them. The final step in the evolution of the route of today's B was the Chrystie Street connection, completed in 1967, which connected tracks on the north side of the Manhattan Bridge to the new Sixth Avenue express tracks. This was a major step in the unification of the system. Trains from Coney Island, over the West End Line and through the Fourth Avenue Subway could now cross the Manhattan Bridge and continue via Sixth Avenue to Central Park West and the Concourse line, as they do today. When letters were introduced for the new lines, this route was initially assigned to the D Train, with the B route running over the Brighton Line like today's D.

The West End/Fourth Avenue//Sixth Avenue route was later reassigned to the B. From the early 90s until a few years ago, during late night service periods the B didn't follow the Central Park West line but rather traversed the 63rd street tunnel to Queensbridge. Later a shuttle replaced the B as the late night service provider to Queensbridge, and currently the B runs on the West End line from Coney Island to 36th street, Brooklyn, and express from there to 145th street, Manhattan all times except late nights, and is reduced to a shuttle serving only the old West End Line portion from Coney Island to 36th street during late nights.

The B line currently runs exclusively R68 stock, disgusting 75' cars from the early 80s with mirrored interiors.

There are major changes in store for the B. Construction will close the south side tracks on the Manhattan Bridge, and the B will likely be rerouted to the north side tracks, which connect to Canal Street and the Broadway line. It will probably run in two segments, a southern one as far as 34th Street on the Broadway line, and a northern one including the Upper West Side portion.