Larson attended Kearney High School in Kearney, Nebraska, but is a native of Funk, Nebraska. He saw action at center, linebacker, and punter, and as a senior, he won All-State honors at punter after averaging 46.5 yards per punt. In addition to football, Larson competed in track and field. Larson was a member of Kearney High's 1999 Class A State Championship team where he placed 2nd in discus and 3rd in shot put at the Nebraska State Track Meet.

Larson was a walk-on at the University of Nebraska. Following a redshirt season in 1999, he backed up starter Dan Hadenfeldt in 2000. He then started from 2001–2003. He was a semifinalist for the Ray Guy Award his junior year, and finalist his senior year, as well as being named an All-American by the American Football Coaches Association. He benched 405 pounds his senior year and hang cleaned 458. As a senior in 2003, he set the Nebraska record with a 45.1-yard avg. on 66 punts, the record would later be broken by Sam Koch. Larson also earned All-Big 12 honors. He graduated with a degree in business administration.

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