Before the 1995 season, Fernández signed a two-year contract with the New York Yankees. It was because of an injury early in the season to Fernández that Derek Jeter was called up to the major leagues for the first time. Fernández injured his elbow during spring training in 1996, and missed the entire season.
Fernández was awarded four consecutive Gold Glove Awards for his defense, 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. Fernandez hit for the cycle as a New York Yankee on September 3, 1995, against the Oakland Athletics. He set a nine-year record for shortstops with a .992 fielding percentage in 1989, while still holding the single-season fielding percentage record for third basemen with .991 in 1994.