Morgan played as a centre-forward. He signed his first professional contract in 1980 with A.F.C. Bournemouth, and went on to make over 400 appearances for a variety of clubs in the lower leagues. In 1984 he joined Bristol City for a fee of £10000. He scored several times that season helping Bristol City secure promotion to the Third division.
Morgan's first coaching role was as assistant to Terry Cooper at Birmingham City. He had previously been signed by Cooper four times as a player. He followed Cooper to Exeter, but left when the club went into administration. His next job was in Australia, as a coach at Perth club Sorrento. During this time, he took Australian citizenship. After four years, he moved to Singapore as manager of Sengkang Punggol FC. He returned to Sorrento before being offered the role of Development Coach at Hull City by former Bolton Wanderers colleague Phil Brown.
During the summer of 2010, Morgan signed for Kingfisher East Bengal F.C. of the I-League in India. It did not take him long to make his mark as during his first competition with the club he won the tournament. This tournament was the Federation Cup where he managed East Bengal to victory over their rivals Mohun Bagan A.C. in the Final.In the same season East Bengal also won Kolkata Premier League and Mohammedan Platinum Jubilee Cup and finished 2nd in I-League.
In the 2011–12 I-League, Kingfisher East Bengal F.C. finished runner-up and turned up as second placed in the Federation cup having won the IFA Shield later. East Bengal managed to a gain the Super Cup too that season. On 14 May 2012, he guided East Bengal to win the Kolkata Premier League, making it three trophies for the season but resigned on the same day after the match citing differences with club officials. Officials continued to talk to him to reinstate Morgan as the coach for next season and finally came to a conclusion and Morgan agreed to coach the Kingfisher East Bengal for the next (2012–2013) season. Kingfisher East Bengal F.C. have won the Federation Cup and Calcutta league under him but he had failed to win the I-League on his last season with East Bengal . Under his guidance the club remained unbeaten at a stretch, for a record of 30 times in a calendar year, finally getting defeated in their home ground. He gained international wideframe, defeating Tampines Rovers 2- 4 in the former's home ground in Singapore on 4 March 2013. Also under his mentorship, East Bengal reached quarterfinals of 2013 AFC Cup with an unbeaten record, a feat that no other Indian club has achieved in the history of this competition.
On 9 April 2013, he announced that he will be leaving Kingfisher East Bengal as he wants to spend time with his family who reside in Perth. He said that his decision for leaving was not money.
On 23 May 2013, under his coaching Kingfisher East Bengal won the Calcutta Football League for the 34th time (3 times in a row). On the very day he announced officially that he is leaving East Bengal after 36 months of coaching. He was the most successful foreign coach of East Bengal and one of the most successful foreign coach of Indian football .He was succeeded by Marcos Falopa.