Founded in 1913 as CD Basconia, it was initially a separate club, first reaching the national championships (Tercera División) thirty years later. It played six seasons in Segunda División (1957–63), but this was before the creation of Segunda División B.
In 1997 Baskonia became Basque neighbours Athletic Bilbao's feeder club, not being eligible for promotion if the reserves, Bilbao Athletic, playing in the above level, did not attain the same goal. Several first-team players made the gradual transition before eventually playing in La Liga and European competition.