Fowler signed for Queen of the South as first team player-coach on 27 June 2014. He was appointed caretaker manager of the club in September 2014, after Jim McIntyre moved to Ross County. Later that month he was appointed manager on a permanent basis.
Fowler was capped twice in 2000 by the Scotland under-21 team. In February 2007, Fowler was rewarded for his development with a late call up to the Scotland B squad against Finland. He played the last 25 minutes in a 2–2 draw at Rugby Park, his club's home ground.