The war intervened in September 1939 with Chester unbeaten after 3 games of the new season, and Chester joined a regional league alongside the likes of Manchester United, Liverpool, Everton and Manchester City. When league football resumed, Chester finished the 1946–47 season in 3rd place and won the Welsh Cup the same year.
The war interrupted Chester's early season progress, but they joined a regional league alongside other top teams like Manchester United, Liverpool, Everton, and Manchester City. After football resumed, Chester finished third in the league and won the Welsh Cup that year.