Following his move to Liverpool, Stubbins scored 28 goals (24 league goals) in the 1946–7 season (making him joint top scorer with Jack Balmer) helping Liverpool to win the League Championship, their first in 24 years. Stubbins also scored 24 goals the following season. Although a contractual dispute in the 1948–9 season limited his appearances for the Merseyside club, he then helped Liverpool reach the 1950 FA Cup Final, the first time Liverpool had appeared at Wembley. However, they lost to Arsenal by two goals to nil.