Born in Ashton-under-Lyne, Lancashire, Whalley first played for Stalybridge Celtic before transferring to Manchester United on 7 May 1934. He made his debut for Manchester United in 1935 as a left-half. The war years prevented him from making more than the 35 appearances he ultimately accrued. Upon Matt Busby's appointment as manager in 1945, Whalley was made first-team coach. After chief coach Jimmy Murphy officially became assistant manager to Busby in 1955, Whalley was promoted to the role of chief coach.
Whalley was played by actor Dean Andrews in the 2011 television drama United, which centred on the successes of the Busby Babes and the decimation of the team in the Munich crash.