Pemberton coached Nottingham Forest's reserve team to the Central League title in the 2007–08 season. In December 2008, following the dismissal of first-team manager Colin Calderwood, Pemberton was appointed as caretaker manager for the match against Norwich City, guiding Forest to a 3–2 victory. Billy Davies was appointed to the post, but did not take over with immediate effect. Pemberton took charge of the Forest side which caused an upset in the Third Round of the FA Cup by winning 3–0 at the City of Manchester Stadium against Premier League opponents Manchester City. At the end of the 2008–09 season Davies reorganised his coaching staff, and Pemberton's contract was terminated by mutual consent after more than a decade as part of Forest's backroom team.