At inter-county level, O'Connor was part of the successful Kilkenny minor team that won the All-Ireland Minor Championship in 1981 before later winning an All-Ireland Under-21 Championship with the under-21 team in 1984. He joined the Kilkenny senior team in 1991. From his debut, O'Connor was ever-present as a defender and made 23 Championship appearances in a career that ended with his last game in 1998. During that time he was part of two All-Ireland Championship-winning teams – in 1992 and as captain of the team in 1993. O'Connor also secured three successive Leinster Championship medals and a National Hurling League medal. He was joined on the Kilkenny senior team by his brother, Willie O'Connor.