Cleland was assistant manager to Steve Morrison at East Stirlingshire before joining Partick Thistle in January 2004. On 21 June 2004, Cleland was appointed as youth coach at Livingston.

Whilst at Livi he served as caretaker-manager role on two occasions, firstly after the dismissal of Allan Preston in November 2004. Cleland led the side to a 3–1 win away to Kilmarnock on 27 November, ended a seven-game losing run. Then following the sacking of John Robertson in April 2007 which ultimately led to him leaving the club a month later when he failed to become permanent manager.

After leaving Livingston, Cleland coached part-time at Rangers in their Academy before being appointed youth coach at Inverness Caledonian Thistle in January 2008. Following their relegation, Cleland was released as a coach by Inverness Caledonian Thistle to cut costs but shortly afterwards took up a similar position at St Johnstone.  He served as their caretaker manager in October 2011, after Derek McInnes and Tony Docherty left for Bristol City. In June 2018, Cleland was promoted to the position of assistant manager at St Johnstone. He was again put in caretaker charge of St Johnstone in May 2020, after the resignation of Tommy Wright.