The last scheduled passenger train on the Brill Tramway left Quainton Road in the afternoon of 30 November 1935. Hundreds of people gathered, and a number of members of the
Oxford University Railway Society travelled from Oxford in an effort to buy the last ticket. Accompanied by firecrackers and fog signals, the train ran to Brill, where the passengers posed for a photograph. Late that evening, a two-coach staff train pulled out of Brill, accompanied by a band bearing a white flag and playing Auld Lang Syne. The train stopped at each station, picking up the staff, documents and valuables from each. At 11.45 pm the train arrived at Quainton Road, greeted by hundreds of locals and railway enthusiasts. At the stroke of midnight, the rails connecting the Tramway to the main line were ceremonially severed.
Quainton Road remained open, but with the closure of the Brill Tramway it was no longer a significant junction. A connection between the GCR and the former Buckinghamshire Railway at Calvert was opened in 1942, leaving the A&B route to Verney Junction with no purpose other than as a diversionary route. It was closed to passengers on 6 July 1936. London Transport passenger services beyond Aylesbury were withdrawn, leaving the former GCR (part of the London and North Eastern Railway after 1923) as the only passenger services to Quainton Road.
London Transport reduced the A&B route between Quainton Road and Verney Junction to a single track in 1939–40. LT continued to operate freight services until 6 September 1947, when the Quainton Road–Verney Junction route closed altogether,[note 14] leaving the former GCR route from Aylesbury via Rugby as the only service through Quainton Road. London Transport services were briefly restored in 1943 with the extension of the Metropolitan line's London–Aylesbury service to Quainton Road, but this service was once more withdrawn in 1948.
The line through the station was reduced to a single track in the 1960s
Quainton Road closed to passengers on 4 March 1963 and to goods on 4 July 1966. On 3 September 1966 the GCR line from Aylesbury to Rugby was abandoned, leaving only the stretch from Aylesbury to Calvert, running through the now-closed Quainton Road, open for freight trains. This was reduced to a single track shortly afterwards. The signal box at Quainton Road was abandoned on 13 August 1967, and the points connecting to the goods yard were disconnected.