Horan made his Munster debut in the 1999–00 season, and was part of the winning team that saw Munster crowned Europeans Champions in
2006. He managed to recover from a calf injury that he picked up in training six weeks prior to the final, and played a role in the
Heineken Cup final, where Munster defeated Biarritz 23–19. Horan also played an integral part in Munster's
Heineken Cup victory at the Millennium Stadium, Cardiff on 24 May 2008, when Munster were crowned European Champions for the second time, defeating
Toulouse 16–13. He lost his place in the Munster team to
Wian du Preez but remained an important part of the team, frequently being sprung from the bench and occasionally starting. A broken hand in October 2010 and an irregular heartbeat meant Horan was out for four months. He made his comeback from injury against
Edinburgh Rugby on 18 February 2011, and won back the number 1 jersey, starting against
Ospreys and
Leinster as Munster secured the
2010–11 Magners League. He became the seventh Munster player to earn 200 caps for the club in a
Pro12 game against
Ospreys on 3 December 2011. Horan agreed terms for a one-year contract extension with Munster in March 2012. On 11 April 2013, Horan announced his intention to retire from professional rugby at the end of the 2012–13 season. His last game for Munster was the
Pro12 fixture against
Newport Gwent Dragons on 19 April 2013. ==Ireland==