He started his career as a junior at Manchester United but was released in June 1983. He signed for Chadderton F.C., then Rochdale before moving to Crewe Alexandra in 1985. He initially came to prominence when he joined Crystal Palace in 1988, helping them win promotion to the First Division in 1989. He appeared for Palace in the 1990 FA Cup Final against Manchester United. The initial tie was drawn 3–3 after extra time, with United winning the replay 1–0 after extra time. In 1990, Pemberton transferred to Sheffield United. During his début against Liverpool in the season opener, he was forced to play in goal after an injury to the United keeper. His most memorable moment came in 1993 when he scored the winning penalty in the shootout against Blackburn Rovers in the quarter-final replay in the FA Cup. The following summer, he was sold to Yorkshire rivals Leeds United. Pemberton became something of a cult figure at Leeds owing to his determination and high work-rate. He appeared in a second Wembley final when he played for Leeds in the 1996 League Cup Final against Aston Villa; again, unfortunately for Pemberton, his side was defeated. He ended his career back at Crewe Alexandra with two appearances in the 1997–98 season.
Managerial career
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. The following season saw him join Crystal Palace's coaching staff for a short spell. The Eagles were in administration, and Pemberton was brought in, along with manager Paul Hart and assistant Dougie Freedman, for two months to keep the Eagles in the Championship. This was achieved on the final day of the season, after which his contract expired. After leaving Palace he was appointed as the manager of Sheffield United's Academy in May 2010 and guided his young team to the Youth FA Cup Final the following season, losing out to Manchester United over two legs. He left Sheffield United in September 2012. On 25 October 2012 he re-joined the coaching staff of Nottingham Forest as a 'Professional Development Coach'. On 28 November 2013, Pemberton was appointed caretaker manager at Bristol City for the club's next game away to Preston North End the following Saturday, this was after the sacking of manager Sean O'Driscoll. He joined Chesterfield as their new academy manager in September 2018, before becoming caretaker manager of their first-team in the following December after Martin Allen was sacked. In May 2019 he was announced as new manager of Kidderminster Harriers. He resigned on 27 November 2019 after five wins in 16 games. In January 2020 he was made caretaker manager og Chesterfield following the sacking of John Sheridan. He was made permanent manager in February.