Horan made his international debut against the USA during the 1999–00 season, but did not win another cap until the 2002–03 season, which came against Fiji. He lost his place to Reggie Corrigan during the 2003 Rugby World Cup and the 2004 and 2005 Six Nations Championship, but consistently strong performances for Munster saw him regain his place in the team. He held down his place for the 2006, 2007, 2008 and 2009 Six Nations Championship, starting every match of Ireland's victorious Grand Slam campaign. He was also an integral part of Eddie O'Sullivan's 2007 Rugby World Cup squad. He missed the 2009 November Tests after having heart surgery, and lost his place to Cian Healy, who held on to the loosehead-prop position during the 2010 Six Nations Championship. Horan played against the Barbarians F.C. and New Zealand Maori during Ireland's 2010 Summer Tests, but was ruled out of the 2010 November Tests with a broken hand. He missed the 2011 Six Nations Championship, but was selected in Ireland's training squad for the 2011 Rugby World Cup warm-ups in August 2011. He played against Scotland, but missed out on selection in the final squad for the World Cup.