Whalen, who will wear No. 81 with the 49ers, was drafted by the Cincinnati Bengals in the sixth round of the 2011 NFL Draft. He appeared in 17 games over three yeas with the Bengals and had 11 receptions for 80 yards. He was released in August of 2014 and then signed by the Minnesota Vikings a year later, but only spent a month with his new team before being released on September 5, 2015.
Whalen played college football at Stanford, where he appeared in 48 games with 27 starts throughout his four-year career.