In August 2011, it was reported that Burnley rejected an offer of £2.5 million from Portsmouth for Paterson. He was again plagued by injury during the 2011–12 campaign, with a thigh problem picked up in August keeping him out until December and then a pulled hamstring picked up January keeping him out until the middle of February. He again picked up a hamstring tear in August 2012, but recovered quickly and went on to score eight goals in 39 appearances in the 2012–13 campaign. However manager Sean Dyche used him primarily as a winger, and speaking in February 2013, Paterson joked that "it's pretty hard to get a game centre-forward - I'll possibly have to shoot Charlie to get a game if I'm honest". Wolverhampton Wanderers attempted to sign Paterson on loan the following month, but were rebuffed by Dyche. Paterson rejected Burnley's offer of a new contract in the summer.