After leaving Chester, he spent time in non-League football with Runcorn F.C. Halton and Witton Albion. While on the books at Witton, he spent five weeks on trial with Football League One side Crewe Alexandra but was not offered a contract, so he signed for League Two side Accrington Stanley in 2006. Whalley spent almost two years with the Lancashire club, but following his release in the summer of 2008, he returned to non-League, initially with Wrexham. While at Wrexham, he had a short loan spell with Southport where he helped the team to the Conference North play-offs. He subsequently played at Droylsden, where he was part of the team that won the Manchester Premier Cup in 2010, and Hyde before joining Southport again on a permanent basis in January 2011. He was signed by Luton Town in the summer of 2013 for an undisclosed fee, and joined AFC Telford United on loan in 2014. Both Luton and Telford won their respective leagues during the 2013–14 season, making Whalley a winner of both the Conference Premier and the Conference North in the same season. He left Luton in May 2015, later joining Shrewsbury.