After spending four months on loan at QPR, making seven appearances, Lee became Oldham Athletic's first signing of summer 2008. Moving on a free transfer, Lee signed a two-year contract with the Latics, beginning on 1 July 2008. His first game with Oldham came in the League Cup second round in a 3–0 loss to Burnley. On 26 December, he made his league debut for Oldham in a 3–0 win versus Crewe Alexandra, assisting in the final goal by Lee Hughes.