He has previously played in Nippon Professional Baseball (NPB) for the Saitama Seibu Lions, Orix Buffaloes, Yomiuri Giants, and Chunichi Dragons.

He was a pitcher during his days at Itami Municipal Sakuradai Elementary School, playing in a national tournament alongside batterymate Katsuki Yamazaki (who would become a catcher for the rival Fukuoka SoftBank Hawks a decade later).

He worked his way into the starting lineup in his first year (the equivalent of tenth grade in the United States), playing right field that summer and becoming the team's leadoff hitter by his second.

He made substantial improvements in his second season (2002), winning the starting shortstop job at the nigun level and becoming the only player in the league to play all 90 games.

He finished the year with a .258 batting average, four homers and 11 RBI, and was given the uniform number 3 during the off-season as a testament to the organization's hopes that he would become the successor to former shortstop and franchise player Kazuo Matsui, who left for the New York Mets via free agency.

On May 7 2005, in an interleague game against the Hiroshima Toyo Carp, Nakajima took a grounder that took a bad hop to the face, breaking his cheekbone and missing a significant amount of playing time.

Rebounding from a disappointing 2005 campaign, Nakajima led all players with a .390 batting average in interleague play in 2006 and was chosen to the All-Star team for the second time in his career.

However, he was hit by a pitch by Tohoku Rakuten Golden Eagles right-hander Hiroki Yamamura on July 30, breaking the fourth metacarpal bone in his left hand.

[8] He hit .343 and led the league in batting average in the first half of the season,[9] playing in the All-Star Game for the fourth time of his career (though he was relegated to third base due to the selections of shortstops Munenori Kawasaki of the Hawks and Tsuyoshi Nishioka of the Chiba Lotte Marines and committed an error on a bad throw) and even seeing time as the team's cleanup hitter when teammates and resident power hitters Craig Brazell and G.G.

He was chosen to the Best Nine that year and even prompted many sportswriters to name him the league Most Valuable Player (though the award eventually went to Eagles ace Hisashi Iwakuma, who went 21–4 with a 1.87 ERA).

[16] As of March 25, 2013, Nakajima was batting only .150 with one double and one RBI in spring training, and John Shea of the San Francisco Chronicle correctly predicted that he would be sent down to the minor leagues.

Some commentators speculated that Nakajima would need to improve his defense, e.g., learning how to move faster toward the ball on MLB's grass infields and being more aggressive around the bag, before his play was up to Major League standards.

[21] In December 2014, Nakajima announced that he had reached a three-year agreement with the Orix Buffaloes, citing frustration at not being able to make the Athletics' major league roster as the reason for wanting to return to Japan.

[24] Chosen to the Japanese national team for the first time in the 2008 Beijing Olympics,[25] Nakajima was expected to platoon at third base with veteran Shinya Miyamoto as a result of fellow middle infielders Munenori Kawasaki and Tsuyoshi Nishioka (who both had better defensive reputations than Nakajima) being chosen, but ended up playing at his natural position from the second game onwards due to Kawasaki's injury in the first game of the tournament against Cuba.

Nakajima played in the second World Baseball Classic as a member of the national team, batting second behind leadoff man and current New York Yankees outfielder Ichiro Suzuki.