Founded in 1993 it last played in Tercera División – Group 3, holding home games at the Campo Municipal Mies de Cozada sports ground, which they share with a Segunda Regional football side (Juventud Atlético San Román) and a División de Honor rugby club (Independiente Rugby Club).

In 1993, the original Rayo was dissolved in a national move to formally absorb affiliated teams into the professional clubs' structure, and Racing de Santander B took its place.

[2] The new Deportivo Rayo Cantabria, who started playing as an independent club in the regional leagues from 1993, was also affiliated to Racing four seasons, from 2003–04 to 2006–07.

The club was excluded from competing in the 2018–19 Tercera División due to unpaid debts,[4][5] and did not enter any competitions in 2019–20 either.

In their absence, in summer 2019 Racing de Santander successfully applied to have their B-team renamed as Rayo Cantabria going forward.