As a young man growing up in Puerto Rico, the athletic Williams developed strong interests in baseball and classical guitar. He was also active in track and field, winning 4 gold medals at an international meet at the age of 15. He was one of the world's best 400-meter runners for his age. On his seventeenth birthday, September 13 1985, he signed a professional contract with the New York Yankees' organization. Playing for the Yankee's Double-A team in Albany, he continued to develop his athletic skills - particularly in the coveted area of switch hitting. Although viewed as a great prospect by the Yankees' management, his rise to the majors was delayed by the solid outfield that the team had developed in the early 1990s. Nevertheless, he managed to break into the majors in 1991 to replace the injured Roberto Kelly for the second half of that season. He batted .238 in some 300 at bats. He was demoted to the minors until Danny Tartabull was injured, and Williams earned his stay at center by putting up solid numbers.

Williams had become the regular Yankees center fielder by 1993. The management of Buck Showalter helped keep him with the Yankees through 1995, when George Steinbrenner sought to trade him. Steinbrenner was frustrated by the team's difficulty in placing him in any of the traditional baseball player molds. He had good speed, but rarely stole bases. In center he was highly capable at tracking down flyballs and linedrives, but had a weak throwing arm. He was a consistent hitter, but lacked home run power. Throughout the early 1990s he hit in the middle of the order as management tried to figure out where he fit in. 1995 was a breakout season for Williams. He hit 18 home runs and led the team in runs, hits, total bases and stolen bases. In the 1996 American League Championship Series, Williams hit a memorable home run in Game 1 and went on to win the ALCS MVP award. The Yankees won the World Series that year, as well as 1998, 1999, and 2000. During the 1998 season, Williams finished with a .339 average, becoming the first player to win a batting title, Gold Glove award, and World Series ring in the same year. After that season Williams inked a seven year, $85 million, contract with the Yankees. The last year covered by his contract, 2005, proved to be a difficult one. He started 99 games in center field and 22 games as a designated hitter, but his already weak arm was highlighted as his fielding and batting abilities considerably weakened. As expected, the Yankees announced on August 2, 2005 that they would not pick up the $15 million option on Williams' contract for the 2006 season, opting to pay a $3.5 million buyout instead. In December Williams was offered arbitration by team general manager Brian Cashman to allow an additional month for negotiation. On December 22, the Yankees re-signed Williams to a 1 year, $1.5 million contract. Bernie Williams was one of the Puerto Rican players to agree to play for Puerto Rico in the 2006 MLB World Baseball Classic, joining Carlos Delgado, Carlos Beltran, Mike Lowell, Javier Vazquez and Jose Vidro amongst others representing the US Territory Island Nation in a team managed by Saint Louis Cardinals third base coach Jose Oquendo.