Born in Evesham, after leaving the British Army, he joined Waterlooville for the start of the 1987–88 season where, after two games for the reserves, he was quickly promoted to the first team and became the club's top goalscorer in the 1987–88 season. One of his goals came in the first round proper of the F.A.Cup against Aylesbury United. He then spent a season at Yeovil Town before, in the summer of 1989, he was signed by Portsmouth, where he then spent the majority of his career, scoring 99 times in 173 league appearances, including Pompey's all-time scoring record of 42 league goals in the 1992–93 season as the club missed out on automatic promotion to the Premier League on goals scored. He was known while at Fratton Park as "Corporal Punishment". In 1993 he signed for Aston Villa in the Premier League. He had a good run in the team and scored important goals against Everton, Arsenal and Sheffield United, before leaving on loan in February 1994 to join Wolverhampton Wanderers; this meant he missed out on Villa's victory in the 1994 Football League Cup Final. In December 1994 he joined Sheffield Wednesday, proving to be very popular at the Owls. Whilst at Wednesday he had a second loan spell at Wolves, as well as being loaned to Watford and Portsmouth who he would later rejoin permanently in 1999. At Portsmouth during his loan spell his seven goals in nine matches helped the club avoid relegation to the third tier. In the 2000–01 season, his last as a professional, he scored for three different clubs, notching for Peterborough United, Oxford United and Wycombe Wanderers. He also featured in Wycombe's FA Cup semi-final against Liverpool. This was the second time that Whittingham had been denied in an FA Cup semi-final by the Merseyside team, having lost in a penalty shootout to Liverpool whilst at Portsmouth in 1992.
Management and coaching career
Whittingham later went on to become player-manager of Newport, but left them in May 2005 when the club ran into financial difficulties. He returned to management at AFC Newbury but when that club suffered financial difficulties and the loss of their ground, Whittingham left in June 2006. In August 2006 he took up a coaching role at Eastleigh. In January 2009, he joined the Portsmouth first-team coaching staff as development coach. He was named joint caretaker manager of Portsmouth together with Stuart Gray on 14 October 2011, when Steve Cotterill left to become manager of Nottingham Forest. The next day the pair won their first game in charge against Barnsley 2–0 at Fratton Park. Whittingham once again became caretaker manager of the south coast club following Michael Appleton leaving to take the vacant position at Blackpool, and stayed as caretaker until the club exited administration in April 2013, with his full-time appointing imminent. On 25 November 2013, Whittingham was relieved from his duties following a meeting with the Portsmouth board.. The 2–1 loss to Southend proved to be his last game in charge on the south coast. Whittingham was appointed first team coach at Crawley on Friday 13 December 2013. Whittingham left the club in April 2014 when it was "mutually agreed" that his contract would not be renewed. Whittingham joined the FA as a coach educator on 1 August 2014.