He attended Franklin Central High School in Indianapolis, where he played for head coach Mark James.

Johnson was named to the Indiana All-Star Team with future NBA players, Eric Gordon, Jeff Teague, Robbie Hummel, and E'Twaun Moore.

[1] The 6'10", 215 lb forward/center committed to the Purdue University Boilermakers to play under head coach Matt Painter as part of a top five recruiting class, along with fellow Indiana All-Stars Robbie Hummel, E'Twaun Moore and Scott Martin.

He helped the Boilermakers to a second straight NCAA tournament appearance, including a game against Baylor in the first round, where he scored 10 points, grabbed 8 rebounds and blocked 2 shots in 20 minutes.

Johnson led Purdue to the program's first Big Ten tournament championship and was named to the all-tournament team and helped lead them to a Sweet Sixteen appearance.

Johnson considered entering the 2009 NBA draft, but made a verbal commitment to return for the junior year.

Johnson was named the Big Ten Player of the Week in late January, averaging 22.5 points and 9.5 rebounds in two games (2–0).

Finishing with a 14–4 record in conference play, Johnson led Purdue to its first Big Ten title in fourteen years, climaxing with a road win against Penn State, where he had 21 points, 10 rebounds, 3 blocks, and shot 11–14 at the line.

With Purdue receiving a 4 seed in the NCAA tournament, Johnson led the Boilermakers in the First Round victory against Siena, where he had 23 points, 15 rebounds, and 3 blocks, leading to consecutive Sweet Sixteen appearances after beating Texas A&M in overtime.

In his final game of his junior season, Johnson had team highs with 23 points, making 10 of 17 attempts, while tallying 5 rebounds and 4 blocks in a losing effort against Duke.

Johnson ended this junior season with the second most career blocks in school history with 184, after Joe Barry Carroll's 349 from 1977 to 1980.

Johnson, along with teammate E'Twaun Moore, entered the 2010 NBA draft, but withdrew and returned to school after scouts projected him as a second-round pick.

JaJuan was named a Sporting News midseason first-team All-American, along with the likes of Nolan Smith, Jordan Hamilton, Kemba Walker, and fellow Big Ten player, Jared Sullinger.

With a 3 seed in the NCAA tournament, Purdue faced St. Peter's in the First Round, where JaJuan scored 16 points and grabbed a career postseason-high 16 rebounds.

[9] Johnson finished his career at Purdue as the seventh highest scorer in school history (1,919), averaging 13.7 points, 6.1 rebounds, 2 blocks, .7 assists, and .7 steals.

On February 12, 2012, in a 95–91 win over the Chicago Bulls, Johnson shot 6-of-13 for a season-high 12 points to go along with four rebounds, two steals and a block.

[14] On November 2, 2012, Johnson was selected by the Fort Wayne Mad Ants with the first pick in the 2012 NBA Development League Draft.

[18] In August 2013, Johnson signed with Giorgio Tesi Pistoia of the Lega Basket Serie A; he helped lead them to an 8th-place finish in the league standings and a spot in the playoffs.

In a home game vs the Slovenian club KK Olimpija, he scored a game-high 20 points and ended with 8 rebounds and 5 steals.