Though born in Corpus Christi, Texas, Freese was raised in the Greater St. Louis area and he grew up a fan of the St. Louis Cardinals. He graduated from Lafayette High School in Wildwood, Missouri, in 2001. Freese recorded a .533 batting average with a total of 23 home runs during his senior season, which remains a Lafayette record. He was considered to be the best shortstop in the state.

Freese was offered a baseball scholarship to play college baseball for the Missouri Tigers baseball team. However, during his senior season at Lafayette High School, he decided to quit baseball. He felt burned out on the sport and opted not to take a baseball scholarship. He enrolled at the University of Missouri, where he studied computer science and pledged Sigma Alpha Epsilon.

Following his freshman year at Missouri, Freese worked for the Rockwood School District maintenance department for the summer. When he visited Lafayette High School towards the end of the summer, he realized how much he missed baseball. Freese contacted Tony Dattoli, the coach at St. Louis Community College-Meramec, to ask for a roster spot.

In one season at St. Louis Community College (2004), Freese hit .396 with 41 RBI's and 10 home runs and was named to the NJCAA All-America second team. Coach Dattoli recommended Freese to Steve Kittrell, the head coach of the Jaguars baseball team at the University of South Alabama. At South Alabama, opposing teams respected his hitting ability, with scouts telling their pitchers: "Don't let Freese beat us." In 2005 as a junior, Freese hit .373, with a .443 on-base percentage (OBP), .525 slugging percentage (SLG), and 52 runs scored in 56 games. He was seventh in the Sun Belt Conference (SBC) in average and led the school one year after Adam Lind had done so. Freese was even better in 2006, hitting .414 with a .503 OBP and .661 SLG with 73 runs and 73 RBI in 60 games. He won the SBC batting title and also led the conference in RBI. He tied for 9th in NCAA Division I in RBI, was 12th in average and just missed the top 10 in runs scored. He made the All-Conference team at third base and was named SBC Player of the Year. He was named an American Baseball Coaches Association All-American as the top third baseman in NCAA Division I, ahead of Evan Longoria and Pedro Alvarez, among others. Kittrell considers Freese to be the best player he coached at South Alabama, where he also coached Lind, Luis Gonzalez and Juan Pierre.