Fernandez was first scouted by the Toronto Blue Jays' famed Latin America scout Epy Guerrero and was signed as an undrafted free agent. Promoted to the Blue Jays in 1983, Fernandez became the team's full-time shortstop in 1985, and probably contributed significantly to the team winning its first division title that year. Fernandez continued to star for the Jays for several years afterwards.
Before the 1991 season, Fernandez was traded to the San Diego Padres in a major deal that also sent Jays star Fred McGriff to San Diego in exchange for Roberto Alomar and Joe Carter. Fernandez played well for San Diego for two years and then began the 1993 season with the New York Mets. After a disappointing start, he was dealt back to the Blue Jays. He played extremely well for the remainder of the season and was instrumental in helping the Blue Jays win the 1993 World Series. In that World Series, Fernandez drove in nine RBIs, a record for a shortstop.
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A very thin man, Fernandez had a tilted, wavering batting stance that made it appear as if he might not be strong enough to hold his bat. From early in his career he carried a scar on his right cheek from a pitched ball. Fernandez was a noted fitness fanatic; he liked buying unusual home exercise machines and trying them out in the clubhouse.
Early in his career Fernandez was well known for his exceptional defensive skills at shortstop. He was especially famous for leaping into the air while simultaneously throwing to first on balls hit far to his right.
Fernandez was awarded four Gold Gloves for his defense, each year from 1986 to 1989. Fernandez was also named to five All-Star teams. He finished his career with a .288 batting average in 2,158 games played, and batted .327 in postseason play.