In the early phase of his coaching career, Wacker coached at Texas Lutheran University, North Dakota State University, and Southwest Texas State University. He won four national championships, two at Texas Lutheran and two at Southwest Texas State.
TCU
Wacker became head football coach of Texas Christian University after the 1982 season. He had early success at TCU. In 1984, his team was ranked as high as #12, the TCU Frogs' highest ranking since 1960, and was invited to the Bluebonnet Bowl after an 8–3 record in the regular season. The #12-ranked Frogs lost a showdown for the Southwest Conference title with the #10-ranked Texas Longhorns on November 10 in what remains the third best-attended game in the history of Amon G. Carter Stadium. After the season, Wacker was named as National Coach of the Year by ESPN, the UPI, and The Sporting News. He was awarded the 1984 Bobby Dodd Coach of the Year Award. There was much hype surrounding the Frogs going into the 1985 season, and Wacker appeared on the cover of Dave Campbell's Texas Football alongside his All-Americanrunning back, Kenneth Davis, a finalist for the Heisman Trophy in 1984 and a leading candidate for the award in 1985. After the first game of the season, Wacker discovered that several players, including Davis, had been benefiting from a payment plan in violation of NCAA rules. Wacker promptly kicked the players off the team and self-reported the infractions to the NCAA, cementing his reputation as a man of integrity. In 1986, the NCAA slapped TCU with three years' probation and a ban on postseason play in the 1986 season. The most severe penalty in the long run, however, was a reduction to only 25 scholarships in 1987 and 1988. To this day, Horned Frog fans remain bitter that the NCAA imposed such a severe penalty given that the violations were voluntarily reported. As heavy-handed as this penalty was, the NCAA seriously considered banning the Horned Frogs from bowl games and live television for three years and no new scholarships in 1987 or 1988. However, it praised Wacker for taking swift corrective action once the violations came to light, including kicking the players off the team when he was well aware that it would cripple the team for the upcoming season. Wacker brought the team back to success in 1990, when the 5–1 Frogs returned to the top 25 for the first time since 1984, before slumping after a season-ending injury to their starting quarterback. In 1991, TCU finished 7–4 for their first winning season since 1984. However, blowout losses to Texas and Texas A&M kept the Horned Frogs out of a bowl. This was one of only three winning seasons TCU had from 1985 to 1997.
Minnesota
Wacker served as head coach at the University of Minnesota from 1992 to 1996. Although he had a disappointing won-lost record at Minnesota, for three years his teams led the conference with academic all-conference honors.
