Funeral trains from London to Woking Cemetery first ran in 1849. The opening of Brookwood Cemetery (and the associated London Necropolis railway station close to London Waterloo) led to an increase in the funeral traffic. A branch line left from the main line station to serve two stations within the cemetery, Brookwood Cemetery North and Brookwood Cemetery South. In June 1863, the LSWR agreed to provide a station on the main line, to serve both the adjacent cemetery and Brookwood village; this opened on 1 June 1864.
The station was reconstructed in 1903, with a new down platform, 576 feet (176 m) long, being built to the south of the original. It was connected to the up platform by a new subway, the footbridge being removed. This made room for the double-track main line to be quadrupled; the new tracks through the station (1 mile 70 chains (3.0 km) between Brookwood East and Pirbright Junction) being brought into use on 15 November 1903. New pneumatic signalling between Woking and Basingstoke was provided between 1904 and 1907; the stretch between Farnborough and Woking was brought into use during June–July 1907, and included a new signal box at Brookwood, having 35 working levers. This box, like the previous Brookwood East manual signalbox, was on the down side of the line.
Operation of the Bisley branch was transferred to the War Office on 1 March 1917, but was returned to the LSWR on 8 August 1918.