On 1 December 2017, Fernández was hired as manager of Alavés, which were placed in the last position in the top division at the date of his arrival. His first game in charge took place three days later, and he led the visitors to a 3–2 away win over Girona FC after they trailed 0–2 with 20 minutes left. In 2018–19, his team started well and were in contention for a Champions League place before fading in the second half to finish 11th, and he resigned at its conclusion.