Whelihan again was second-string quarterback in 1998, this time behind second-overall draft pick Ryan Leaf. After a Leaf pick-six put San Diego behind by 19, Whelihan replaced Leaf in the Week 4 (September 27) game against the New York Giants. In his first drive of the game, Whelihan made a 41-yard touchdown pass to Charlie Jones; the ensuring extra point cut New York's lead to 28-16. San Diego lost the game 34-16, and Whelihan finished with 6 of 15 completed passes for 97 yards and a touchdown as well as 13 rushing yards in 3 carries. In contrast, Leaf threw 4 interceptions in the game in 15-for-34 passing for 193 yards.