Thomson started playing at Townhill Boys Club [2]
Thomson made his Dunfermline debut in August 1970 and despite being part of the team relegating from the first division in 1971-72 he played a part in Dunfermline coming straight back up in 1972-73. After the league restructuring and another relegation Thomson played a key role in the club's promotion in 1979 and was presented with the Dunfermline Player of the Year award.[3] However, he was freed by new manager Pat Stanton in 1982.
Thomson joined Alloa Athletic where he helped them achieve promotion in 1984-85 and later St Johnstone who were promoted to the Premier Division in 1990.