Following their return season in which they escaped relegation by a single point, they achieved two wins against Barcelona in the following campaign and would qualify for the UEFA Cup for the first time upon finishing sixth (to date, their highest-ever placing, coming just 12 years after their lowest-ever: eighth in their group in the fourth level).

As well as concluding the domestic campaign in tenth position, in 2000–01 the Basque club reached the final of the UEFA Cup after beating Internazionale,[8] Rayo Vallecano and 1.

[9] The final ended in a 4–5 loss against Liverpool, Alavés losing to an "own-golden goal" after taking the match to extra time.

[10] Alavés ended 2001–02 in seventh position and qualified for the UEFA Cup for a second time, although the European campaign of 2002–03 was far less successful than two years earlier, with an opening win over Ankaragücü followed by a defeat to another Turkish Süper Lig side, Beşiktaş.

[9] In this time, Alavés was bought by Ukrainian–American businessman Dmitry Pietrman, and several clashes followed with the club's coaches, players[11] and fans alike.

A subsequent black period in Segunda B lasted four years until Alavés was bought by José Antonio Querejeta[13] and were promoted again to the second division in 2013 as overall champions of the third tier, providing an opportunity to sort out its economic difficulties.

Three years later, on 29 May 2016, Alavés was promoted to La Liga as second tier champions after beating Numancia 2–0 to overtake Leganés on the final day.

[14] On 7 February 2017, Alavés qualified for the 2017 Copa del Rey Final after eliminating Celta de Vigo in the semi-finals of the competition.

Their opponents in the final would be Barcelona, and coincidentally the two clubs met in the league directly after their cup semi-finals; the Catalans inflicted a 6–0 defeat on Alavés in their own Mendizorrotza Stadium, exacting revenge for the result earlier in the season.

[15] Barcelona also won the final, held at the Estadio Vicente Calderón with a 3–1 scoreline,[16] meaning there would be no return to European competition for Alavés.

[17] In the 2021–22 season, Alavés were relegated following defeat on the penultimate matchday by Levante (who also went down) to end their six-year stay in La Liga, the longest top-flight run in the club's history.

The club's primary reserve team is Deportivo Alavés B, founded in 1960 and currently playing at the amateur Tercera División level of the senior Spanish system.

[37] In April 2018, Alavés signed an agreement with French club FC Sochaux-Montbéliard;[38] however the partnership lasted only a few months, ending abruptly in December of the same year.

[39] In June 2018 Alavés took a controlling interest in another Croatian top-tier club, NK Istra 1961, a few weeks after ending their agreement with Rudeš.