Wharton spent his childhood at the Academies at Liverpool and Everton, before he came through the academy at Tranmere Rovers to sign professional forms in January 2017.[1][2] He joined Northern Premier League Division One West team Colwyn Bay on loan on 18 August 2018.[3] He made his debut later that day, keeping a clean sheet in a 1–0 victory over Kendal Town at Llanelian Road.[4] He played seven games for the "Seagulls" before returning to Prenton Park; Bay manager Craig Hogg said that "both players [Wharton and Jay Devine] have been excellent to work with and are a total credit to their club".[5] On 9 October, Wharton made his senior debut for Tranmere in a 6–0 defeat at Shrewsbury Town in the group stages of the EFL Trophy.[6]
On 22 October, he joined Northern Premier League Premier Division side Stalybridge Celtic on a one-month loan deal after "Celts" goalkeeper Jake Turner picked up an injury.[7] He made seven appearances for Simon Haworth's "Bridge", before he returned to Rovers in November. He immediately joined Northern Premier League Premier Division side Marine on loan.[8] He made ten appearances for Neil Young's "Mariners". On 7 January 2019, he returned to Stalybridge Celtic for his second loan spell of the season at Bower Fold, this time joining until the end of the 2018–19 season.[9]
He was released by Tranmere at the end of the 2018–19 season.[10]
In December 2019 he joined Atherton Collieries on loan.[12] During the loan he played in the FA Trophy, which lead to FC United stating they would never play him again after the loan expires as they had agreed a Gentlemen's agreement that he wouldn't play in the FA Trophy.[13] Wharton denied this agreement existed and called the situation a disgrace.[14]