Burnett started his managerial career with Fisher Athletic in 2004, winning the London Senior Cup and Southern Football League Eastern Division. He then joined Dulwich Hamlet in 2006. He was appointed manager of Fisher Athletic for the second time in May 2007. On 23 September 2008, it was announced that Burnett would join Conference side Grays Athletic as manager on 29 September. He left the club by mutual consent on 29 January 2009. Burnett briefly worked as the youth team manager at former club Leyton Orient before it was confirmed on 7 May 2009 that Burnett would take up the position of assistant manager to John Still at League Two club Dagenham & Redbridge for the forthcoming 2009–10 season. On 26 February 2013 Burnett was appointed caretaker manager following Still's departure to Luton Town. On 2 May 2013, following Dagenham & Redbridge's survival in League Two, Burnett was appointed permanent manager.