Lee played with Waterford Junior side Carrick United before signing for Wexford Youths in January 2015. He made his senior debut for the Youths in a Leinster Senior Cup match against North End United on 22 February and his league debut came two weeks later against Cabinteely on the opening night of the 2015 season. He quickly settled into the centre of defence and made 25 league appearances for the club as Wexford won the league title and were promoted to the Premier Division.

Lee remained at Wexford in 2016 and made a total of 45 league appearances during his two seasons at Ferrycarrig Park before signing for Shane Keegan at Galway United in December 2016.