Horgan made his Munster debut against Connacht in August 1997. He started for Munster in their first Heineken Cup final against Northampton Saints in May 2000.Horgan was also selected to start the 2002 Heineken Cup final loss against Leicester but broke his hand the night before in a captains run. Due to his withdrawal John O'Neill started in his place He was part of the Munster team that beat Neath to win the 2002–03 Celtic League, and he picked up more silverware when Munster beat Scarlets to win the Celtic Cup in May 2005. Horgan started for Munster as they beat Biarritz 23-19 to win their first Heineken Cup final in May 2006.