Hendrickson's first coaching job was at Georgia Tech as an assistant to Bill Curry in 1983. As part of the Georgia Tech coaching staff, Hendrickson won a national championship in 1990. In 1992, he was hired at the University of Iowa as an assistant to Hayden Fry. Following a brief stint at Southeast Missouri State University, he returned to Iowa, and was shortly thereafter hired as an assistant at Western Illinois. Hendrickson served as Offensive Coordinator from 1999 to 2007. While part of the Leatherneck coaching staff, WIU appeared in the playoffs in 2000, 2002, and 2003. He was named acting head coach in 2008, and later head coach in 2009. Hendrickson led the Leathernecks to the Division 1-FCS playoffs in 2010, where they won over Coastal Carolina and lost to #2 Appalachian State. The 2010 Leathernecks ended the 2010 season #17 in the The Sports Network final poll and #20 in the FCS Coaches poll. Hendrickson finished second in the final voting for the 2010 Eddie Robinson Award, awarded by The Sports Network .