Due to the war the normal competitions were suspended, with Pompey still holding the FA Cup won in 1939. Pompey recorded their all time record win in all competitions a 16 - 1 win against Clapham Orient in the London War Leagues. Later in 1942 Pompey lost 2-0 to Brentford in the London War Cup final.

The glory years

Pompey finally lost the FA Cup when it was contested again in the 1945/1946 season. League football resumed for the 1946/1947 campaign. 1948 was Pompey's golden jubilee year and will be one to go down in the history books, Pompey were almost the first club to win a league and FA Cup double, but Pompey lost to Leciester 3-1 in the semi final. Making up for this Pompey stormed to win the league that year, also in this year Pompey had their record attendance of 51,385 against Derby in the FA Cup 6th round. The 1949/1950 season was also a sucessful one, sharing the Charity Shield with Wolves after a 1-1 draw, then retaining the league championship beating Aston Villa 5-1 on the last day of the season, becoming one of a very select band of clubs to win the top tier of English football in back to back seasons.

Pompey were also flew high in the 1951/1952 season finishing fourth, but in the summer of 1952 the championship winning manager Bob Jackson left to join Hull City FC. With an aging squad, and the youth coming through not being good enough to replace them the team was starting to struggle, although Pompey finished a respectable third in the 1954/1955 season, the only way from then was down, ending in relegation at the end of 1959.