He played in the Central League from 1998 to 2006 and won six Golden Glove awards at third base. He also hit 106 home runs in his last three seasons in the Central League, including 32 (with a .311 batting average) in 2006. His best season was 2004, when he hit 44 home runs with 103 RBI and a .300 batting average. In that same season, he also set the Japanese baseball record for strikeouts with 173.
During the 2006 offseason, Iwamura opted to be posted for Major League Baseball. The posts were due to the commissioner of Major League Baseball on November 10, 2006; the highest bidder would be granted the right to negotiate a contract with Iwamura. Incidentally, Daisuke Matsuzaka, who signed a six-year, $52 million contract with the Boston Red Sox that same year, is a close friend of Iwamura.
On December 15, 2006, Iwamura signed a three-year contract with the Rays worth $7.7 million, with a club option for a fourth year at $4.25 million.