The 1939–40 Segunda División season, the first after a three-year hiatus caused by the Spanish Civil War, saw 40 teams participate in the second flight Spanish league. Murcia was promoted to Primera División. RD Oriamendi, Sestao, Alavés, Erandio, Granollers, Ferroviaria, Imperio de Madrid, Mallorca, Constancia, Elche, Alicante, Burjassot, Imperial de Murcia, Ceuta SC, Onuba and Tánger were relegated to Tercera División due to a Federation decision.