Dundee born goalkeeper John Thomson played for Shettleston before joining hometown Scottish League club Dundee in 1920, from where he was signed by Third Division (South) club Gillingham in July 1921, making his Football League debut at Southampton that August. Sharing goalkeeping duties with Jack Branfield, Thomson played in 26 of the club’s 46 fixtures during the campaign, but after starting the following campaign as the incumbent he lost his place to Fred Fox and moved on to join Barrow in July 1923 after 39 appearances for The Gills.
At Barrow he shared goalkeeping duties with Norman Wharton, making 19 appearances during their 1923-24 campaign before being signed in March 1924 by Second Division Nelson, as cover for Harry Abbott. Thomson played twice the same month, both matches against Barnsley, including playing in a 4-3 home win, a rare success in a season which saw Nelson suffer relegation in their only Second Division campaign. Thomson then returned north of the border and joined non league club Glasgow Benburb.