He matriculated to Princeton University, after an injury late in his senior year caused other Division I schools to withdraw their offers.
He led the Ivy League in field goal percentage three times and ranks third all-time in Princeton history in that statistic for his career.
The team earned three consecutive Ivy League championships during his career, including an undefeated conference record during his senior season.
Despite the team's success and his individual accolades, his Princeton tenure was punctuated by three NCAA tournament first-round losses by a total of seven points, most notably the March 17, 1989 NCAA Division I men's basketball tournament first-round 50–49 Georgetown vs. Princeton men's basketball game loss to the number-one seeded Georgetown Hoyas team featuring Alonzo Mourning and Dikembe Mutombo as well as 1989 Big East Conference Men's Basketball Player of the Year Charles Smith.
As a junior, his outside shot was still undeveloped,[1] but he averaged 20 points and 10 rebounds, leading his team to the 1986 Des Plaines Valley League championship and a second straight trip to the sectional finals.
[3][4] He was benched for one game in early March of his junior year for disciplinary reasons by coach Dick Flaiz.
[7] Following the school year, he played in the suburban summer basketball league at Triton College in River Grove, Illinois.
[16] By the end of his senior season, he was one of the 20 All-Chicago Area selections by the Chicago Sun-Times, in a class that included Eric Anderson, Bond, Liberty and Sam Mack, after averaging 23 points and 14 rebounds.
[19][21] Division I schools like Northwestern University withdrew their scholarship offers;[18] however, Princeton maintained an interest, with supporters like John Rogers behind him.
[18] As most of his scholarship offers were withdrawn, he began to focus on schools that could provide him an academic opportunity in the event that his basketball career was over.
[19] As a freshman, Mueller helped the 1987–88 Tigers win their final three games in March to finish the season with a 17–9 (9–5 Ivy League) record.
[28] During his sophomore season, the 1988–89 team earned a #1 vs. #16 matchup in the first round of the 1989 NCAA Division I men's basketball tournament with their Pete Carril-coached princeton offense.
[30] During the game, Mueller played beyond the foul line on the offensive end, forcing Mourning to leave passing lanes open for back-door attacks.
[31] Although the strategy enabled Princeton to stay in the game, Mourning had seven blocked shots, including two in the final fifteen seconds.
[22] Later in the same tournament, Duke would use Christian Laettner at the top of the key, like Princeton had used Mueller, and eliminate Georgetown by shutting down Mourning.
[39] As a junior, Mueller earned a third team Academic All-America recognition from College Sports Information Directors of America.
[41] The team went undefeated in the Ivy League and earned a berth in the 1991 NCAA Division I men's basketball tournament.