Whalen was born in Portland, Oregon. He attended La Salle High School in Milwaukie, Oregon. In football, he finished his senior season with 68 receptions for 1,502 yards and 18 touchdowns, receiving Tri-Valley League Player of the Year and all-state honors. He was an all-state basketball selection and also lettered in baseball.
He moved on to Shasta College, where he had one undistinguished season. 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 sophomore, he had seven receptions. The next season, he was converted from wide receiver to tight end, recording 23 receptions and 3 touchdowns. As a senior was 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. He set NCAA records for most receptions in a season and most receptions per game (8.2) by a tight end. 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. His 10 receiving touchdowns in a season at the time ranked second in school history.
The Tampa Bay Buccaneers selected him in the fifth round (157th overall pick) of the 2000 NFL Draft, after dropping because he lacked size and speed. He was waived on August 27, after being passed on the depth chart by undrafted free agent Todd Yoder.
In 2000, the Dallas Cowboys signed Whalen to their practice squad and promoted him to the active roster for the last 3 games of the season. The next year, he was allocated to the Scottish Claymores of NFL Europe, where he led the league in receptions (66) and also had 691 receiving yards and 3 touchdowns. On September 23, 2001, he was placed on the injured reserve list with a strained right Achilles.
In 2002, he was a core special teams player and tallied 15 tackles. In 2003, he suffered hamstring and ankle injuries that limited him to playing in only 9 games and registering 7 special teams tackles. He was released on July 26, 2004.
On July 28, 2004, the Cincinnati Bengals signed him as a free agent. He was cut on September 5.
On February 22, 2005, he was signed as a free agent by the Philadelphia Eagles to compete for a backup tight end position. He was released on August 28.