The 1998–99 season was the 67th in the history of Real Zaragoza and their 21st consecutive season in the second division.

The club participated in La Liga and the Copa del Rey.

Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.

Players may hold more than one non-FIFA nationality.

Source: Competitions Source: La Liga Zaragoza entered the competition in the third round.