Whelihan signed with the af2 team San Diego Riptide on January 27, 2005. Never playing a game for the Riptide, Whelihan returned to the AFL in March 2005 and signed with the Las Vegas Gladiators. With Las Vegas, Whelihan started 2 of 14 games and was mainly a holder when not a starter. He completed 58 of 92 passes for 684 yards, 13 touchdowns, and 2 interceptions. In 2006 with the Gladiators, Whelihan played all 16 games and started 5 and made 131 of 223 passes for 1,677 yards, 30 touchdowns, and 11 interceptions as well as 5 rushing touchdowns.