Founded in 1983, it ceased to compete in 1996 and returned in 2011, holding home games at Complejo Deportivo San Amaro, with a capacity of 1,000 spectators.

In the 1989–90 Segunda Division season, Real Burgos managed to finish in first place and promote to La Liga for the first time, just seven years after its foundation as a professional club.

In its first season in the top tier, Real Burgos surprised many by finishing in the 11th place, with 37 points and a positive goal difference of +5.

The team even managed to steal points from the best in the league, by beating Real Madrid at home 2–1, and drawing against Barcelona away 0-0.

In 2018, Real Burgos sued the Castile and León Football Federation, claiming a place in Tercera División alleging irregularities in the announcement of the fixtures during the last rounds of the 2017–18 season.