Gannon began his playing career at Dundalk, but moved to English club Sheffield United in 1989. The next year he transferred to Stockport County, following a short loan spell with Halifax Town. He spent the next ten years at Stockport, becoming one of the club's most loyal servants, and helped the club to second-place finishes in both the Second Division and Fourth Division, as well as two League Trophy finals. After leaving the club in 2000, he spent a season with Crewe Alexandra, before returning to Ireland with Shelbourne, winning two League of Ireland Premier Division titles in his three years there.