Javier spent his first season in the Oakland Athletics' organization with the Huntsville Stars, with whom he won the Southern League baseball championship. He made his Oakland A's debut in May 1986, prior to that playing with the Tacoma Tigers, the Oakland A's Triple-A Pacific Coast League affiliate. Javier remained with the club as a fourth outfielder through the 1988 season, in which the A's captured the American League West crown. Javier batted .500 in his first post season, going two-for-four in both the 1988 American League Championship Series with the Boston Red Sox and World Series with the Los Angeles Dodgers.