Alavés competed in La Liga, the top flight of Spanish football, in 1998–99 for the first time since 1955–56, having won promotion as Segunda División champions in the previous season, which was their first under head coach Mané.

In the Copa del Rey, they failed to match their heroics of the previous year, when they reached the semi-finals.

[2] They received a bye to the third round, where they were eliminated on away goals after a 2–2 aggregate draw with Segunda División side Las Palmas.

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

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