The next year, he walked on at the University of Kentucky, after showing head coach Hal Mumme a highlight video tape made by his mother.
As a senior he had a breakout season, being recognized as a consensus first-team All-American, after registering 90 receptions for 1,019 yards and 10 touchdowns, leading the tight ends in all three categories nationally.
His 90 receptions broke the school's single-season record and became the first tight end and second Kentucky player to top 1,000 receiving yards in a season.
Whalen was selected by the Tampa Bay Buccaneers in the fifth round (157th overall pick) of the 2000 NFL draft, after dropping because it was considered he lacked size and speed.
On August 30, 2000, the Dallas Cowboys signed Whalen to their practice squad and promoted him to the active roster on December 5, for the last 3 games of the season.
In 2003, he suffered hamstring and ankle injuries that limited him to playing in only 9 games (2 starts) and registering 7 special teams tackles.