After leaving Newcastle and joining Bury in February 1961, Stokoe spent a short time as a player, leading the team in an undefeated run to promotion, before making the move into management with the same club as player-manager the following season.

Stokoe took the post of player-manager at Bury in December 1961 which, at 31 years of age, made him the second-youngest manager in the Football League.

At the time, he declined, preferring to stay with Carlisle; just over eighteen months later, however, he became the ninth official manager in Blackpool's history.

Stokoe agreed to sell Tony Green to his old club, Newcastle, bringing striker Keith Dyson in the opposite direction.

However, Sunderland scored in the first half through Ian Porterfield and with the help of a memorable second-half match-saving double save from goalkeeper Jim Montgomery, managed to win 1–0.

Stokoe is remembered for his impromptu jubilant run down the pitch at the end of the game, complete in Mackintosh and his trilby hat, to celebrate the victory with Montgomery.

A statue of Stokoe with his arms held aloft in celebratory mid-run now stands outside Sunderland's Stadium of Light.

After being unwell for some time with Alzheimer's disease, Stokoe was admitted to hospital in Hartlepool suffering from pneumonia and died on 1 February 2004 aged 73.

The Reverend Neil Cockling, the Methodist Minister for Prudhoe, who conducted the service, told mourners: "He will be remembered by all as a real gentleman.