Handed the Kansas City Royals' starting shortstop job in 2003 after the departure of Neifi Perez in spite of hitting a disappointing .194 in the previous season's Dominican Winter League, Berroa started the season hitting ninth in the batting order and committing 19 errors in his first 63 games. However, he finished the season with a .287 batting average with 17 home runs, 73 runs batted in, 21 stolen bases, and committed only five more errors the rest of the season.
Late in the season, manager Tony Pena moved Berroa to the top of the batting order, and Berroa's performance sparked a media debate whether he or New York Yankees outfielder Hideki Matsui, a former star in the Japanese Central League, should win the Rookie of the Year Award.
In a controversial decision, Berroa beat out Matsui in the closest vote since 1980, prompting criticism from Yankee owner George Steinbrenner. While some players and sports writers believe veteran Japanese players who come to play baseball in the United States should not be considered rookies, Major League Baseball rules allow them to win the award. Debate over the definition of a rookie aside, Berroa's backers pointed to their identical batting averages and Berroa's greater home run total while hitting in a weaker Kansas City lineup and playing a more demanding position. Matsui's backers pointed to his higher RBI total while playing in the media spotlight of New York City.
Berroa became the fourth member of the Royals to win the award, following Lou Piniella (1969), Bob Hamelin (1994) and Carlos Beltran (1999).
Berroa was acquired in 2001 from the Oakland Athletics in a three-way trade also involving the Tampa Bay Devil Rays. Kansas City acquired Berroa, relief pitcher Roberto Hernandez, and backup catcher A.J. Hinch in exchange for fan favorite Johnny Damon and infielder Mark Ellis.