Wallner graduated from Forest Lake Area High School in Forest Lake, Minnesota, where he played baseball. As a junior, he committed to play college baseball at the University of North Dakota. However, during his senior year, North Dakota dropped baseball for financial reasons, and he then signed with the University of Southern Mississippi. As a senior, he pitched to a 7-1 record with a 0.95 ERA along with batting.382 with ten home runs and was named Minnesota Mr. Baseball. Following his senior season, Wallner was drafted by the Minnesota Twins in the 32nd round of the 2016 Major League Baseball draft. However, he did not sign, and instead chose to honor his commitment to the University of Southern Mississippi. In 2017, as a freshman at USM, Wallner hit.336 with 19 home runs and 63 RBIs in 66 games. He also appeared in nine games out of the bullpen, compiling a 1.84 ERA. He was named Freshman of the Year by Conference USA, Baseball America, and D1Baseball.com. He also garnered Freshman Hitter of the Year honors from the National Collegiate Baseball Writers Association. He was named to the C-USA All-Freshman Team as well as the C-USA Second Team. He was also named a Freshman All-American by multiple outlets including the Collegiate Baseball Newspaper and the NationalCollegiate Baseball Writers Association. As a sophomore in 2018, Wallner batted.351 with 16 home runs and 67 RBIs in 62 games while pitching to a 7.98 ERA in 14.2 innings. He was named to the C-USA First Team and once again was named an All-American by various publications. Following the season, he was named to USA Baseball's Collegiate National Team. He also played in the Cape Cod Baseball League for the Falmouth Commodores. Prior to the 2019 season, Wallner was named a preseason All-American by Baseball America, Collegiate Baseball Newspaper, D1Baseball.com and Perfect Game. During the year, he hit his 54th career home run, becoming USM's all-time record holder. Wallner batted.323 with 23 home runs and sixty RBIs for the season, earning a spot on the C-USA First Team. He finished his collegiate career with a school record 58 home runs. Wallner was selected by the Minnesota Twins with the 39th overall pick in the 2019 Major League Baseball draft. He signed for $1.8 million, and was assigned to the Elizabethton Twins. He was promoted to the Cedar Rapids Kernels in August. Over 65 games between the two clubs, Wallner batted.258/.357/.452 with eight home runs and 34 RBIs.
