As a horsecar and streetcar line

The Brooklyn City Railroad opened the line, a branch of their Fulton Street Line, to the city line on July 14, 1860, and to Vernon Avenue in Flatbush about a week later.^[4] The Vernon Avenue Depot was built on the east side of the line at the terminal.^{[citation needed]} The line was later extended to Bergen Beach along Flatbush Avenue and Avenue N, and later still the line along Flatbush Avenue was extended to Avenue U in Marine Park; the older route became the Bergen Beach Shuttle.^{[citation needed]}

As a bus line

Buses were substituted for streetcars on March 4, 1951.^[5][6]

Limited-stop service was added on September 14, 1992.^[7][8] In September 1996, all trips on the route were slated to be cut back to the alternate terminal at Tillary Street and Cadman Plaza West from Old Fulton Street at Fulton Landing as part of a reconfiguration of service in Downtown Brooklyn.^[9] The change took effect on March 30, 1997.^[10] This 0.6 miles (0.97 km)-long section was eliminated as it duplicated B25 service, because this section was underutilized, with an average of 1.5 passengers per trip, and because the shorter route would increase the B41's reliability. B25 service was made 24/7 to make up for the loss of Sunday service to Fulton Landing.^[9]

On December 1, 2022, the MTA released a draft redesign of the Brooklyn bus network.^[11][12] As part of the redesign, all Bergen Beach branch service would be replaced by the B40, which would run from Bergen Beach to Prospect Park station, making local stops along Avenue N (Veterans Avenue) and limited stops along Flatbush Avenue.^[13] The B41 Limited would be replaced with the B41 Crosstown, which would continue to run from Downtown Brooklyn to Kings Plaza, making limited stops south of Kings Highway.^[14] In Downtown Brooklyn, the B41 and B41 Crosstown would run via Livingston Street, Smith Street, Joralemon Street, Boerum Place, and Livingston Street.^[14][15] Closely spaced stops would also be eliminated.^[15]