[17] Thompson returned to the first team in the new year, making his first league start for Leeds against Burnley in a 2–1 victory on 2 January, playing in central midfield before being moved to right back after an injury to Patrick Kisnorbo.

[18] He retained his place in the starting line for the remaining four games of January, including an impressive defensive display away against Arsenal in the FA Cup, as Leeds slipped to a narrow 1–0 defeat after a late Thierry Henry strike.

[20][21] Thompson lost his place to Smith in the following game and caretaker manager Neil Redfearn first match in charge in what was a comfortable 3–0 victory away to Bristol City.

[22] Thompson would find his opportunities limited for the rest of the season whilst Leeds appointed former Queens Park Rangers manager Neil Warnock to replace Grayson.

[23] After the expiration of Leeds' slim hopes of making the Play-Offs, Thompson returned to the first-team and made his first appearance under Warnock on 6 April 2012 away to Reading.

[24] He lasted 13 minutes in the game before being given a straight red card for a lunging challenge on Jobi McAnuff as a resilient Leeds side went down 0–2 to two late goals from Adam Le Fondre.

[26][27] After appearing for the team in the pre-season summer 2012 schedule, Thompson found himself on the fringes of the squad for Warnock's first full season in charge as fellow young prospect Sam Byram leapfrogged him in the pecking order for the right sided position.

"[34] In the following game versus Yeovil Town at Huish Park, Thompson was given a straight red card on 27 minutes after a two-footed lunge on Keanu Marsh-Brown as ten-men Bury went down 2–1.