[1] After graduating from Santa Teresa High, Whelihan enrolled at Oregon State University and redshirted his freshman year.
[1][2] He ended his college career ranked third on the school's list for completions (300), attempts (591) and TDs (27).
[11] Whelihan again was the second-string quarterback in 1998, this time behind second-overall draft pick Ryan Leaf.
In his first drive of the game, Whelihan made a 41-yard touchdown pass to Charlie Jones; the ensuing extra point cut New York's lead to 28–16.
[13] In Week 6 (October 11), a 7–6 loss to the Oakland Raiders, Whelihan again replaced Leaf late in the game.
[17][18] With 16 seconds left on 4th-and-20, Thelwell caught a 30-yard touchdown pass from Whelihan, and the extra point tied the game at 13.
He began the season with the Memphis Maniax; stuck at third string behind Jim Druckenmiller and Marcus Crandell, the league transferred Whelihan to the Chicago Enforcers midseason to replace Tim Lester.
Whelihan played for three different Arena Football League teams: the Orlando Predators (2001–2002, 2004), the Indiana Firebirds (2003), and Las Vegas Gladiators (2005–2006).
After Orlando started 0–3, Whelihan led the Predators to a four-game winning streak by June 2001.
[24][25] Never playing a game for the Riptide, Whelihan returned to the AFL in March 2005 and signed with the Las Vegas Gladiators.
[1] In 2007, he served as the backup quarterback and holder for the ArenaBowl XXI champion San Jose SaberCats.
In 2003, Whelihan became quarterbacks coach at La Costa Canyon High School of Carlsbad, California.