Fernández 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, Fernández became the team's full-time shortstop in 1985, and probably contributed significantly to the team winning its first division title that year. Fernández continued to star for the Jays for several years afterwards.

Before the 1991 season, Fernández 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. Fernández 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, Fernández drove in nine RBIs, a record for a shortstop.

In 1997 he reached the World Series again, thanks in large part to his own game-winning home run against Baltimore in the American League Championship Series. In 1998 he rejoined the Blue Jays, and revitalized his hitting, batting over .300 both seasons there. In 2001 he briefly played for the Milwaukee Brewers but returned to Toronto late in the season, and retired at its conclusion.

A very thin man, Fernández 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. Fernández was a noted fitness fanatic; he liked buying unusual home exercise machines and trying them out in the clubhouse.

Early in his career Fernández 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.

Fernández was awarded four Gold Glove Awards for his defense, each year from 1986 to 1989. Fernández 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.

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