As a player who was born in the 1980 Japanese academic year and participated in the 1998 Summer High School Baseball Championship, Murata is considered a member of the "Matsuzaka Generation".

Murata enrolled in Nihon University in Tokyo as an economics major alongside his high school batterymate Ohno and worked his way into the lineup as the team's starting third baseman, eventually developing into one of the league's more prominent sluggers.

He tied a Tohto University Baseball League record for most home runs in a single season (previously held by Tadahito Iguchi) with eight that fall.

Murata earned his second straight selection to the Japanese team prior to the 31st Japan-USA University Baseball Championship Series in the summer of his senior year (2002).

Other notable college players selected in the same draft include Tsuyoshi Wada and Nagisa Arakaki (Hawks), Katsuhiro Nagakawa (Hiroshima Toyo Carp), Hirotaka Egusa (Hanshin Tigers) and Gotoh and Chikara Onodera (Lions).

Murata made the ichigun (Japanese equivalent of "major league") roster in the spring of his rookie season in the pros, making his professional debut in the season opener against the Tigers on March 28, getting his first career hit then-Yomiuri Giants veteran Masumi Kuwata on April 1 and hitting his first home run off Giants left-hander Hisanori Takahashi the next day.

5 hitter, but saw fewer starts as the season went on due to his spotty defense and abundance of strikeouts, with then-manager Daisuke Yamashita opting to use veteran Hitoshi Taneda or Seiichi Uchikawa at third base instead.

He hit his first career grand slam off Giants left-hander Tetsuya Utsumi on June 22, finishing the year with a .252 average, 24 home runs and 82 RBI.

He remained in the cleanup spot until the end of the season, finishing with a .266 average, 34 homers and 114 RBI (all career highs) as one of the few consistent sources of offensive production on a team plagued by injuries all year.

He passed then-Chunichi Dragons slugger Tyrone Woods, who had led him by eight homers at the end of August, and finished with 36 (one more than Swallows right fielder Aaron Guiel), leading the Central League in home runs for the first time in his career.

Murata cemented his role as the team's cleanup hitter in 2008,[10] hitting just .231 with six home runs in the month of April but heating up in May and reaching the 30-homer plateau by the end of July.

Murata began the 2009 season with the farm team, unable to play due to a torn left hamstring suffered while running the bases during the World Baseball Classic held in March.

However, he came down with a severe cold and had to be hospitalized in Tokyo in early August, keeping him from taking part in team practices prior to departing for Beijing and temporarily weakening his dynamic visual acuity.

Japan's disappointing fourth-place finish behind South Korea, Cuba and the United States prompted sharp criticism of manager Senichi Hoshino by the Japanese media, who had opted to start Murata in eight of the team's nine games despite his clearly not being in good health and hitting just 2-for-23 (.087) with one double (55th of all 58 qualifying players in batting average) during the tournament.

In early 2009, Murata was chosen to play in the World Baseball Classic as a member of the national team, his first opportunity to redeem himself after an abysmal showing in the Olympics the previous summer.

He played first base in the seeding match in the second round of the 2009 World Baseball Classic (Giants slugger Michihiro Ogasawara took his place after he was injured).