After his release, Fagan began training at the Glenn Hoddle Academy in Spain, leading to a trial period with Huddersfield Town in March 2009,[2] in which he scored a hat-trick on his debut for the club's reserves,[3] before Hamilton Academical signed him at the end of that month.
[7] He scored four times in 17 appearances for Lincoln, but was deemed surplus to requirements at the club after the appointment of Chris Sutton as manager in September 2009, and on 1 February 2010, he moved on loan to Spanish third-tier side Jerez Industrial, with which the Glenn Hoddle Academy had strong links, for the remainder of the 2009–10 season.
[19] Fagan started off well at his new club, receiving the man of the match award at home to Cliftonville, for his superb link up play in the Setanta Sports Cup First Round Second Leg at Richmond Park.
[26] More success followed for Fagan when he scored a brace against Bray Wanderers at the Carlisle Grounds although unfortunately the Saints had two points taken from them by a 94th-minute Jason Byrne equaliser in a 3–3 draw.
[31] He also scored the winner in a 2–1 win in the 105th minute in the second leg, making it four goals in his last four games in the Europa League and earning Pats a tie with Hannover 96 from Germany.
[33] Fagan continued to excel with Pats and he scored the winner in a 1–0 win away to Cork City at Turners Cross to make it to the 10 goal mark in the league.
[36] Flood returned from illness for the trip to both striker's former club Bohemians, but Fagan beat him to the starting spot and opened the scoring after 24 minutes to make it four goals in four games for him, as Pats won 2–0 to go top of the league.
[40] Fagan's final goal of the season came on 26 September 2013 when he scored in the 95th minute to secure a 3–1 win against Bray Wanderers at the Carlisle Grounds in a vital game in the League of Ireland title run-in.
[42] Fagan started the 2014 season brilliantly, winning another trophy in the form of the inaugural 2014 FAI President's Cup, as the Saints beat Sligo Rovers 1–0 at Richmond Park on 2 March 2014.
[46] In July 2014, he scored the opening goal in St. Patrick's' 1–1 draw away to Legia Warsaw in the first leg of their 2014–15 UEFA Champions League second qualifying round tie.
[51][52] He made his debut the next month, coming on for Alan Judge in the 76th minute of a 2–1 win over Spain,[53] followed by another substitute appearance in a 3–0 loss to Turkey in a qualifier for the 2009 UEFA European Under-21 Championship.