2012

Whalen was signed by the Indianapolis Colts as an undrafted free agent following the 2012 NFL Draft on April 28, 2012,^[17] joining fellow Stanford players Andrew Luck and Coby Fleener.^[18] On August 28, 2012, he was put on the injured reserve list for a broken foot, which occurred against the Pittsburgh Steelers.^[19]

2013

More hurdles were thrown Whalen’s way in 2013. His position on the active roster at the beginning of the season was due to second year wide-out LaVon Brazill's four-game suspension due to a violation of the league’s substance abuse policy. Whalen was cut following Brazill’s return, but was quickly signed to the practice squad after impressing the Colts’ coaching staff. He was activated once again after Reggie Wayne’s season-ending ACL injury during the Week 7 victory over the Denver Broncos.^[20]

Following a second spell on the practice squad, Whalen returned to the active roster in Week 15 against the Houston Texans and started to offer a glimpse of the potential at his disposal. A career-high 45 receiving yards and first touchdown catch against the Texans was followed by an 80-yard day in the impressive 23–7 road victory over the Kansas City Chiefs, a game in which Whalen led the Colts in receiving yards and receptions.^[21] His fine run of form continued in the 30–10 victory over the Jacksonville Jaguars in Week 17, adding a second touchdown catch in three weeks.^[22]

Whalen made his playoff debut against the Kansas City Chiefs in the Wild Card Round on January 4, 2014. In the 45–44 victory, he had two receptions for 26 yards.^[23] In the Divisional Round against the New England Patriots, he had five receptions for 67 yards in the 43–22 loss.^[24]

Overall, Whalen ended the year as a starter with 24 receptions for 259 yards and two touchdowns.^[25]

2014

On November 22, 2014, the Colts promoted running back Zurlon Tipton to the active roster and waived Whalen. Up to that point, he had been used mostly as a kickoff and punt returner, and made just 2 receptions for 23 yards.^[26] On November 25 Whalen was signed to the practice squad by the Colts.^[27] On January 15, 2015, Whalen was promoted to the active roster when Josh McNary was placed on the Commissioner's Exempt list.^[28]

2015

On October 18, 2015, against the New England Patriots, Indianapolis coach Chuck Pagano called for a trick play on 4th and 3 late in the third quarter with the Colts trailing 27–21. The play left Whalen accidentally snapping the ball to Colt Anderson with no Colts teammates blocking and two Patriots players standing over the ball. The play was stopped for a loss, the Patriots took over on downs and scored a touchdown en route to a 34–27 victory. The play was questioned by numerous NFL experts and players from around the league. In the game, he did score his first touchdown since the 2013 season with a late score to pull within a touchdown of the Patriots.^[29][30] Just a week later, Whalen was part of a second disastrous special teams play, when he fumbled on a kick return which led to a touchdown in a game against the New Orleans Saints.^[31] Whalen redeemed himself the following week against the Carolina Panthers by catching all five of his targets that came in the fourth quarter, helping send the game into overtime. Against the Denver Broncos, Whalen had 5 receptions for 73 yards, and was a crucial part to the Colts beating the then-undefeated Broncos.^[32] On December 21, 2015, Whalen was placed on season-ending injured reserve.^[33] On January 1, 2016, Whalen was waived by the Colts.^[34]