The San Diego Chargers drafted Whelihan in the sixth round (197th overall) in the 1995 NFL Draft. Whelihan played his first game in Week 8 (October 16) of the 1997 season, in a 31-3 loss to the Kansas City Chiefs. Replacing Stan Humphries, Whelihan completed 2 of 8 passes for 13 yards. In his second game with San Diego, a 38-31 loss to the Cincinnati Bengals in Week 10 (November 2), Whelihan completed 8 of 16 passes for 90 yards and passed for his first NFL touchdown, a 44-yarder to Charlie Jones with 6 minutes left in the 4th quarter.