He was a left-handed first baseman who played in the farm system of the St. Louis Cardinals from 2003 to 2005. In 2003, he started out with the Johnson City Cardinals in the Appalachian League and then moved to the Palm Beach Cardinals in the Florida State League. He also played for the Palm Beach Cardinals in 2004 and 2005. In 2005, he advanced to the Double A level with the Springfield Cardinals in the Texas League.

Schutzenhofer consistently hit over .300 in the minor leagues. From 2000 to 2003, he was a first baseman for the University of Illinois at Urbana-Champaign, setting several school records. He ranks third in all-time career hits with 132 and sixth in all-time career RBIs with 173. His on base percentage was .449, which is fourth best in the history of the Fighting Illini. In 2000, Schutzenhofer set an all-time freshman record with 87 hits and 63 RBIs. He helped the Fighting Illini win the Big Ten Tournament with seven home runs, 63 RBIs, and a .375 average. He was named a Freshman All-American. He was selected to the All-Big Ten first team and the ABCA Midwest Region first team. In 2001, he led his Fighting Illini team with a .392 batting average. He was selected to the All-Big Ten second team in 2001 and 2002. He was chosen for the All-Big Ten first team in 2003. He excelled in athletics and academics. In 2003, he received the Big Ten’s Award of Honor for the Outstanding Scholar-Athlete.

Schutzenhofer played for several summer collegiate baseball teams. In 2000, he was an all-star first baseman with the Alton Bluff City Bombers in the Central Illinois Collegiate League. In 2001, he was selected to the all-star team while playing for the Waterloo Bucks in the Northwoods Summer Collegiate League in Iowa. In 2002, he was with the Kenai Peninsula Oilers in the Alaska Summer Collegiate Baseball League.

From 1996 to 1999, he was a first baseman for Belleville East High School, and his father Dennis was head coach of the team. Their team advanced to the Illinois state tournament in 1996.