Whelihan replaced Humphries as starter effective Week 10 (November 9) because Humphries suffered concussions. In Whelihan's debut as starter, Whelihan completed 17 of 29 passes for 206 yards, 2 touchdowns, and an interception in a 37-31 loss to the Seattle Seahawks. Whelihan also lost a fumble in the Chargers' own end zone, and Michael Sinclair recovered the fumble for a defensive touchdown. In the last play of the game, Sinclair sacked Whelihan to seal the Seahawks win. Playing for only the first three quarters, Whelihan had a season-low 22.2% completion rate in Week 12 (November 23) against the San Francisco 49ers, completing 4 of 18 passes for 81 yards and 3 interceptions before Todd Philcox replaced him. San Diego finished 1997 with a 4-12 record, including 0-7 with Whelihan as starter. In 9 games (7 starts), Whelihan finished 1997 with 118 of 237 passes completed for 6 touchdowns and 10 interceptions, 21 sacks for 168 lost yards, and 29 rushing yards on 13 carries.