The 2006 football team put together one of the most successful seasons in program history. The team rolled through its regular season schedule, finishing with an 11-0 record. The undefeated regular season was the first for the program since 1974, and the team won a Heart of America Athletic Conference championship for the first time since 1999. Highlights from the regular season include three-straight shutouts, over Avila (Mo.), Baker (Kan.) and Culver-Stockton (Mo.), plus a 24-7 win over Benedictine (Kan.) and a 44-17 win over William Jewell (Mo.) to close out the regular season. In the NAIA Football Championship Series, the Vikings opened with a first round win over Bethel (Kan.), 31-14, followed by a quarterfinal win over Northwestern (Iowa), 33-26. The team advanced to the NAIA FCS semifinals for the first time since 1978, but fell to Sioux Falls (S.D.), 25-18, ending the season with a 13-1 record.
The 13 wins is the most all-time for a Viking football team in a single season. Statistically, the team ranked highly in the NAIA in a number of team categories on both offense and defense. The Vikings posted the No. 1 rushing defense in the country (42.5 yards). The team was also No. 2 in sacks per game (3.2), No. 3 in total defense (195.8 yards), No. 5 in total offensive yards per game (414.2 yards), No. 8 in passing offense per game (246.8 yards) and No. 10 in scoring defense per game (12.2 points).
A number of individual awards and honors were handed to members of the team after theseason. Three were named NAIA All-Americans, ten were selected to the all-conference first team, six were selected as second team all-conference, three on the all-conference third team and seven were all-conference honorable mention selections. Larry Wentzel was named both the Heart Defensive Player of the Year and the Heart Player of the Year. Also, Head Coach Paul Troth earned the Heart Coach of the Year award.