In 2009, after a spell out of football McFarland was appointed the caretaker manager until the end of the 2008–09 season of Burton Albion on 6 January, filling the gap created by Nigel Clough who had moved along the A38 to McFarland's former club Derby County earlier in the day. His first game in charge ended in a 3–0 victory for Burton against Salisbury City in the FA Trophy second round; it was a victory which McFarland dedicated to his predecessor. McFarland eventually helped to extend Burton's unbeaten run to 17 games, which dated back to October 2008, before his side were beaten 2–0 by his former team Cambridge United in March 2009. McFarland managed the side to promotion to the Football League, after which he said he was interested in staying at the club for the 2009–10 season. He later turned down the opportunity to continue as manager, as he "did not want the full-time commitment of running a League Two club on a permanent basis." He was eventually succeeded by Paul Peschisolido.