Kerr briefly managed Lincoln City in 1977 and became manager of Grimsby Town in 1979. The Mariners won the Third Division championship in 1980 and finished 7th in the Second Division the following season after challenging for promotion with the side third with seven games remaining, and a return to Division One after a 33-year absence looked very much on the cards, but the clubs form fell away afterwards, with them winning only one more game. That form was not maintained the following season despite a good start, and with Grimsby bottom of the league Kerr was sacked on 11 January 1982 to make way for his assistant, David Booth.
He was appointed manager of Rotherham United on 21 March 1983 but was unable to save the club from relegation to the Third Division. He remained in charge for another two years, first avoiding relegation and then challenging for promotion before finishing mid-table. In November 1983, Rotherham knocked out first division Southampton in the League Cup. In June 1985, Kerr returned to Lincoln where despite the presence of Phil Turner and Neil Redfearn in midfield, the side was relegated to the Fourth Division. He remained in charge the following season, which began well with the Imps as high as 7th in the New Year. An inexplicable collapse in form followed and Kerr left the club in March, before Lincoln became the first club to be relegated from the Football League to the Conference. He later managed Boston United.