Further success followed for O'Connor's youngsters in the early 2000s. Coláiste na Sceilge won three consecutive Corn Uí Mhuirí titles in 2001, 2002 and 2003, however, the team fell in the subsequent All-Ireland semi-final on all three occasions. After a prolonged absence O'Connor guided his school team to a fourth Corn Uí Mhuirí title in 2009. At the fourth attempt Coláiste na Sceilge reached the All-Ireland final. St Mary's of Edenderry provided the opposition, however, the Kerry youngsters were too strong and won the game by 1–9 to 0–10. It was a first Hogan Cup title for Coláiste na Sceilge.