After beginning his career with spells at Wrexham, where he helped win the Football League Trophy in 2005, and Milton Keynes Dons, he joined Peterborough United in January 2007 after a short loan spell, helping the club reach the Football League Championship by winning consecutive promotions in the 2007–08 and 2008–09 seasons.
Morgan began his career as a youth player at Wrexham, making his professional debut at the end of the 2001–02 as a substitute during a 5–0 win over Cambridge United at the age of 16, a game which confirmed Wrexham's relegation to Division Three,[4] and was handed a second substitute appearance the following week in a 1–0 defeat to Stoke City.
The 2003–04 season saw Morgan begin to establish himself in the Wrexham first team, making 21 appearances in all competitions as the club mostly stayed clear of a relegation battle with a 13th-placed finish.
[10] However the season ended in disappointment for the team as they were relegated back into Division Three after being docked ten points due to entering administration.
After starting the next season in the first-team, Morgan fell out of favour and was allowed to return to his first club Wrexham on a one-month loan deal,[17] one week after making his debut for Wales, becoming the first Milton Keynes Dons player to win an international cap since the team's relocation.
[18] He made his debut for The Posh on 2 December 2006 in a 2–1 win over Tranmere Rovers in the second round of the FA Cup as an 85th-minute substitute for Shane Huke.
Ahead of the club's League One campaign in the 2008–09 season, Morgan was handed the captaincy of the team at the age of just 23, taking over from Micah Hyde.
"[24] Despite losing the captaincy,[25] he remained a regular first-team player and helped the side to their second consecutive promotion after forming a defensive partnership with Gabriel Zakuani,[26] finishing as runners-up to Leicester City and reaching the Football League Championship.
During the summer break after the 2008–09 season, Morgan became Peterborough's all-time record international appearance maker by winning his 14th cap for Wales in a friendly against Estonia.
[26] In December 2009, Morgan revealed he nearly joined Notts County loan deadline window, but it fell through at the last minute.
After being sent off over professional foul in a 2–1 loss against Yeovil Town on 28 January 2012, Morgan was partly used due to injury and then falling out of favour by newly manager Graham Westley.
[50] On 12 June 2015, Craig Morgan joined League One side Wigan Athletic on a free transfer on a two-year contract.
He made his debut for the Wales senior side on 11 October 2006 in a 3–1 win over Cyprus at the Millennium Stadium during the qualifying campaign for Euro 2008.