Thomson started playing at Townhill Boys Club Thomson made his Dunfermline debut in August 1970 and despite being part of the team relegating from the first division in 1971-1972 he played a part in Dunfermline coming straight back up in 1972-1973. However he was freed by new manager Pat Stanton in 1982.
He achieved one of the most number of Scottish league appearances, 654, between 1970 and 1992 After the league restructuring and another relegation Thomson played a key role in the clubs promotion in 1979 and was presented with the Dunfermline Player of the Year award. Thomson joined Alloa Athletic where he helped them achieve promotion in 1984-1985 and later Street Johnstone who were promoted to the Premier Division in 1990.
