The war time years of 1939-45 forced the majority of football clubs across the country to close down temporarily. But for Bath City that period provided great names, great football and some stirring memories. City kept going under the indefatigable Arthur Mortimer. A series of friendly matches were staged with visits from Birmingham, West Bromwich and Corinthians. With the establishment of Service Camps in the vicinity of Bath, many famous players eagerly sought a game - most were in the services as PT instructors. Mr Mortimer lost no time in contacting the players. Payment was permitted by the FA of 30 shillings (1.50) per match per player. A galaxy of players arrived at Bath and in consequence tremendous victories were achieved over teams permitted in the area. City won the Football League's second division north in 1944 with a better average over other zones in the country, and the West Cup. Gates soared to over 10,000 on occasion, especially with the visits of Bristol City. International player abounded - City had three international goalkeepers - Vic Woodley and John Jackson (Chelsea) and Sidlow (Wales). Other famous players were: Bill Shankley (former Liverpool manager), Dave McCullock (Scotland and Derby) and Stan Mortensen (England and Blackpool). Mortensen was a member of a Sunderland flying-boat crew who survived when brought down in the Atlantic, and went on to perform brilliantly for England and his Blackpool team. Stan, a great friend of Arthur Mortimer, also played for City in Southern League matches together with McCullock and Teddy Owen. The progress of the war saw the Bath Blitz, in which City's ground suffered, much of the popular side stand was reduced to twisted steel and many cottages at the Bath end suffered badly. The draw for the war time FA Cup was made - the matches to be played on a two leg basis - and City were paired with Aston Villa. The visit of Villa was a great occasion. Despite transport difficulties a crowd of 17,000 assembled on the grassy unterraced banks, part of which had been used for allotments in the war effort. The result was a 3-3 draw with City losing the return match 1-0 before a gate of 30,000 at Villa Park.

With the cessation of hostilities City returned to the Southern League, and the old routine of league fixtures, under various managers, including Vic Woodley and, former England captain, Eddie Hapgood. City made little impression in the league and it was once again the cup competitions in which they excelled. In 1949-50 City reached the final of the Southern League Cup for the first time. Their opponents, Colchester United, were firm favourites after missing out on the League title on goal difference to Merthyr Tydfil, and after winning the first leg at Twerton Park 3-0 this tag seemed justified. However, in a great second leg at Layer Road goals from Snook, Kelly, Mills and, in the last minute, Hawkins gave City a 4-1 lead and took the game into extra time, where United hit back with two goals to win 6-4 on aggregate. The FA Cup saw City gain further success as they beat third division Southend United 3-1 in 1952-53 and Exeter City 2-1 in 1957-58. Also during this period City won the Somerset Premier Cup (1951/52, 1952/53 and 1957/58).

Towards the end of the 1950's financial problems began to plague City once more and with the club in serious danger of folding the board turned to the supporters club for financial and administrative assistance. It was decided that the way to bring the crowds back to Twerton Park was to invest in some 'name' players and, with the maximum wage rule not covering non-league football, the persuasive powers of Mortimer and manager Bob Hewison went to work. The new arrivals included the famous Charlie 'Cannonball' Fleming, signed for a fee of 10,000 from 1st division Sunderland. The Scotland international was joined by Ian Black (Scotland and Fulham), Ian McFarlane (Chelsea), Paddy Hale (Bristol Rovers), Peter Thomas (Cardiff City) and Joe O'Neill (Leicester City). And joining this group was the returning Stanley Mortenson as captain of the team.