Thomson began his career with Edinburgh City and joined Scottish League club Heart of Midlothian in April 1953.[2] He had to wait until February 1957 to make his debut, which came in a 1–1 First Division draw with Falkirk.[3] He went on to make six further appearances during the 1956–57 season and was thereafter a regular in the team until his departure in November 1960.[2] He was a fixture in Hearts' 1957–58 and 1959–60 First Division title-winning teams and featured as an ever-present in the latter triumph.[4][5] He also played in both the 1958 and 1959Scottish League Cup-winning campaigns.[6][7] Thomson made 161 appearances and scored 17 goals during three-and-a-half years as a first team player at Hearts.[2]
Everton
Thomson and Heart of Midlothian teammate Alex Young moved south to join EnglishFirst Division club Everton for a combined £55,000 fee on 26 November 1960.[8][9][10] Thomson was unable to hold a regular place in the team during his 2+1⁄2 seasons with the club,[10] but he managed to make 20 appearances during the club's championship-winning season in 1962–63.[11] He made 77 appearances and scored one goal for the club before departing Goodison Park in late 1963.[10]
Brentford
Thomson joined newly-promoted Third Division club Brentford November 1963 and stayed at Griffin Park for 4+1⁄2 years, before retiring at the end of the 1967–68 season.[9] Thomson made 179 appearances and scored five goals for Brentford.[9]