The club was founded in 1964 as Reyfra Atlético O.J.E. when CD Reyfra (1963–64) and CA Getafemerged. In 1970 it absorbed Aviaco Madrileño CF, which was established in 1967 when Madrileño CF (1956–67) and AD Aviacomerged, became affiliated with Atlético Madrid and changed its name to Atlético Madrileño Club de Fútbol.
In 1991, the name changed to Atlético Madrid B. Having already played from 1980–86 in Segunda División, the reserves fluctuated between that level and Segunda División B – created in 1977 as the new third division – in the following decades. In the 1998–99 season, the team, which featured Rubén Baraja, future Valencia and Spain star in central midfield, finished in second position in division two, but was ineligible for La Liga promotion, so Numancia gained the automatic promotion slot instead.