Morgan began his career at Tranmere Rovers, making his debut on 27 August 1996 in a 2–0 victory over Port Vale before spending time on loan at Conference National side Altrincham.
[4] After a spell with Porthmadog, Morgan took over as player-manager of Welsh Premier League side NEWI Cefn Druids, replacing Steve O'Shaughnessy in February 2004.
[5] However, he spent just 10 months in the role before stepping down in December 2004 and moving to Rhyl, where he made one appearance before ending his first team playing career at Connah's Quay Nomads.
In 2007, Morgan joined Bangor City as assistant manager to former Tranmere player Neville Powell where they led the side to two consecutive top six finishes and UEFA Cup places.
Morgan lead Llandudno to promotion to the Welsh Premier League for the first time in the club's existence after winning the 2014–15 Cymru Alliance.