In 2002 Penney retired to pursue a career in management and he remained at Doncaster, taking the managerial job on a full-time basis. After a well-placed finish in his first season, Penney guided Doncaster back into the Football League with victory in the 2003 play-off final. Their stay in Division Three wasn't long though as he managed Doncaster to the Division Three title. During a further two seasons of cementing Doncaster's place in League One Penney famously masterminded victories over Premier League sides Manchester City and Aston Villa, and nearly overcame Arsenal in the League Cup quarter-finals before finally being beaten in a penalty shootout. Penney left Rovers on 30 August 2006 as he felt he had taken the club as far as he could. He was appointed manager of Darlington on 30 October 2006. He returned to Doncaster with Darlington for a Football League Trophy tie on 9 January 2007, Doncaster winning the game 2–0, and Penney received a hero's reception from the home fans at the new Keepmoat Stadium. Penney was appointed manager at Oldham Athletic on 30 April 2009. He left on 6 May 2010, through mutual consent, with falling attendances one of the reasons why Penney was relieved of duty. On 10 January 2011 Penney was appointed as manager of League One club Bristol Rovers. His tenure in charge of the west country club did not last long however, as he was sacked less than two months later having lost nine of his 13 games in charge. His last game was a 2–0 defeat against Dagenham and Redbridge. Following receiving the sack from Bristol Rovers, Stuart Campbell was put in charge for the game against Tranmere, in which a Chris Lines goal sealed a 1–0 win. While at the Memorial Stadium, he only recorded two wins, against Swindon Town and Oldham Athletic, and also recorded a 6–1 defeat away to Walsall. He was reported as being furious after being overlooked for the Grimsby Town managerial job when Rob Scott and Paul Hurst were appointed on 22 March 2011. As of 13 May 2013, he is reported to be interested in a coaching role at Southend United, as newly appointed manager Phil Brown seeks to improve the quality of back-room staff at the club. He was hired as an assistant coach, leaving the position in June 2015. In September 2016, Penney was once again hired as an assistant manager, this time for Guiseley. Together with manager Adam Lockwood, Penney was fired on 30 August 2017. On 1 October 2017, York City hired Penney as a sporting director.
Personal life
Penney's son, Mark Penney, is a semi-professional footballer, with his clubs including Glasshoughton Welfare.
