Following the ski season, Stenerud joined the football team for spring drills in 1965 and as a junior that fall he kicked a 59-yard field goal, then a college football record, in a 24–7 home win over rival Montana. In 2013, Stenerud recalled that he had a significant tail-wind aiding him on that kick in Bozeman; the ensuing kick-off went over the end-zone bleachers at Gatton Field, whose elevation exceeded 4,900 feet (1,495 m) above sea level. He was named an All-American by The Sporting News as a senior in 1966, and was also an All-American in ski jumping and a three-time Big Sky champion.

The Chiefs were the final AFL champions in 1969, and they met the NFL Champion Minnesota Vikings in Super Bowl IV in New Orleans. The underdog Chiefs won 23–7, and Stenerud kicked three field goals, scoring the first nine points of the game. His first, a 48-yarder, was the longest field goal in a Super Bowl for 24 years, exceeded by Steve Christie of the Buffalo Bills in Super Bowl XXVIII in January 1994.

On Christmas Day 1971, the Chiefs hosted the Miami Dolphins in an AFC divisional playoff game. In perhaps his toughest day as a professional, Stenerud made a 24-yard field goal in the first quarter, but then missed from 29 and 32 yards, the latter with 35 seconds remaining in regulation, and had a 42-yarder blocked three minutes into overtime. The Dolphins won 27–24 in double overtime on a 37-yard field goal by Garo Yepremian. Through 2017, the game remains the longest in NFL history at 82 minutes, 40 seconds of playing time, and was also the final football game in Municipal Stadium.

Enshrined in 1991, Stenerud, along with George Blanda, Lou Groza, Ray Guy, and 2017 inductee Morten Andersen, is one of only five kicking specialists in the Pro Football Hall of Fame, and is one of three who did not play another position (Blanda played quarterback, Groza was a tackle). The Chiefs retired Stenerud’s jersey number 3 in his honor. In 1994, he was selected to the NFL’s 75th Anniversary Team.