On the opening day of the season, Lonergan made his debut for Leeds in the 3–1 defeat against Southampton. Lonergan received the man of the match award in Leeds' 1–0 loss against Middlesbrough on 14 August. Lonergan started his fourth game of the season against Hull City at Elland Road where he put in another good performance making saves to deny Hull City as Leeds United won 4–1. After some good performances for Leeds in his first couple of months at the club, Lonergan revealed that the move to Leeds had worked out "brilliantly" for him. Lonergan made some crucial saves for Leeds to help earn them a 3–2 victory against Crystal Palace on 10 September. Lonergan saved a penalty from Nicky Maynard on 17 September against Bristol City to help Leeds earn a 2–1 victory. Lonergan got his first clean sheet of the season against Portsmouth on 1 October, with Lonergan again making some crucial saves. After keeping a consecutive clean sheet, Lonergan was substituted in the second half against Doncaster Rovers after fracturing his finger and replaced by Paul Rachubka on 14 October. Lonergan missed the game against Coventry City with the finger injury on 18 October and was replaced by understudy Paul Rachubka. After the game manager Simon Grayson revealed Lonergan had surgery on the finger and would be ruled out for a minimum of six weeks.