Founded in 1913, Basconia reached the national third level (Tercera División) thirty years later. The club played in the second tier for six seasons (1957–63), but this was before the creation of the regionalised new third division in the 1970s.
Basconia’s place in Athletic's club structure means that the squad changes greatly each season. About half of the players move up to play for Bilbao Athletic, or go out on loan to other local clubs playing at Segunda División B level. They are replaced by graduates, usually 17 or 18 years old, from the previous year's Juvenil A team. The squad is normally expanded further with new signings from the regions’s youth clubs, most notably Danok Bat and Antiguoko.
Although the players and coaching staff of the main squad are controlled by Athletic Bilbao, Basconia retains its own club committee and staff and operates several youth teams as well an amateur side (Basconia B) who compete in the Preferente de Vizcaya league, two levels below the first team. These other teams play in a separate small stadium in the town, Soloarte. Occasionally the main squad has been supplemented by some of Basconia's 'own' players in emergencies - Mikel Rico was with Basconia B when he appeared in one Tercera División fixture in 2001. He left Biscay for a long career across Spain which eventually brought him back to the senior team of Athletic in 2013.