The league placings have largely mirrored the fortunes of the senior team. From their formation in the 1960s until the late 1990s, Alavés B competed only in the fourth (Tercera Grupo IV) or fifth (Preferente de Álava) tiers. They achieved promotion to Segunda División B in 1999, a year after the seniors climbed to La Liga. Alavés B remained in the third level for seven seasons, usually finishing mid-table, until demotion in 2005-06, the same year that the main side was relegated amid economic turmoil under Dmitry Piterman.
The decline of the club continued and the senior side themselves dropped into Segunda División B in 2009, while the B team were relegated back down to the fifth level. It took Alavés B only two seasons to regain fourth-level status whereas the seniors took four years to rise again to the second level, but they then gained promotion to La Liga after three further seasons while the B team stayed put in Tercera División from that point on.