McPherson returned to Falkirk, in 2009, as academy technical director. In 2014, McPherson became assistant manager of his old club Morton, and signed a two-year extension in May 2016. After leaving Morton following
Jim Duffy's sacking, McPherson became first team coach at
Scottish League One side
Dumbarton in September 2018, but left the club following
Stephen Aitken's sacking. He then returned a fortnight later as assistant manager following Duffy's appointment as Aitken's successor. McPherson began working with the
Rangers Women's team in July 2021, as an assistant to manager
Malky Thomson.
Police Scotland opened an investigation in March 2023 after McPherson appeared to headbutt
Celtic manager
Fran Alonso following a match between the two clubs. The
Scottish FA charged McPherson under its rules regarding violent conduct for the same incident, and subsequently banned him for six games. ==Honours==