Johnson considered entering the 2009 NBA draft, but made a verbal commitment to return for the junior year. He began his junior season as a preseason first team all-Big Ten selection by CBS Sports. In the season, he recorded nine double-doubles, while leading Purdue to its best start in 16 years (14–0). 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). On February 9, 2010, Johnson recorded his 1,000th career point in a road game win against #10 ranked Michigan State. 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. In an average of 31.3 minutes a game, Johnson averaged 15.4 points (3rd on team), 7.3 rebounds (1st), and 1 steal per game. Johnson shot 72 percent at the line, while leading the top ten ranked Purdue squad with 2 blocks a game and shooting 51 percent from the floor. Johnson was named "Second-Team All-Big Ten" and received consecutive "Big Ten All-Defensive Team" honors at the end of the regular season. 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&amp;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 held the third highest average in school history with 1.7 blocks per game, behind Carroll and Russell Cross. He spent the following summer practicing with Team USA.