He fell out of favour at Ulster under head coach Alan Solomons, who left him out of the squad for the 2001–02 Heineken Cup."Ulster axe winger Cunningham", BBC Sport, 19 September 2001 His final appearance for the province came in December 2002, after a series of injuries left the team short of centres for a Heineken Cup tie against Biarritz Olympique,Gavin Mairs, "Go out there and blitz Biarritz: Cunningham", Belfast Telegraph, 27 October 2005 scoring a try in a narrow defeat."Ulster beaten by Biarritz", RTÉ Sport, 14 December 2002 His contract was up at the end of the 2002-03 season, and he was not offered a new one.Gavin Mairs, "European Cup heroes lose Ulster contracts", Belfast Telegraph, 11 February 2003 He had made 54 appearances for the province. He resumed his legal career as a trainee solicitor with Millar McCall Wylie, rising to become a partner at the firm in 2011.Jan Cunningham profile at Millar McCall Wylie His younger brother Bryn also played for Ulster,Bruce McKendry, Champions: The Players' Story, IRFU (Ulster Branch), 1999, p. 140 and has been the team's Operations Director since 2015.Richard Mulligan, "Ulster management happy with progression across all fronts", News Letter, 15 December 2015
