Charlie Thomson was born in Perth, Perthshire in 1905. He played for St Johnstone YMCA and for Scottish League clubs Alloa Athletic and Falkirk where he spent four seasons, before moving to England to sign for Brighton & Hove Albion in 1934. He was a first-team regular for five years and made 191 appearances for the Seagulls.
Charlie joined Exeter City in 1939, and played in the first three matches of the 1939-40 Football League before competitive football was abandoned for the duration of the Second World War. He then returned to Scotland where he played for Dundee United in the Eastern Regional League and was on the losing side in the Scottish War Emergency Cup, won by Rangers. After the war, he rejoined Exeter City before going back to Scotland.