Racing de Santander played its first match on 23 February 1913, losing 1–2 to neighbouring Strong. It was officially founded on 14 June, as Santander Racing Club, appearing in its first tournament during that summer (Luis Redonet Trophy) and being admitted to the Northern Federation on 14 November, eventually merging with Santander Football Club.

In 1929 Racing first reached La Liga, lasting nine consecutive seasons in the category – finishing in second position in its third year – and fluctuating between the first and the second divisions (with four participations in the third) in the following 30 years. In 1950 the Cantabrians returned to the top flight after a ten-year absence, scoring 99 goals in only 30 games.

During the period of Francoist Spain, the club was renamed Real Santander in 1941, because of the prohibition of non-Spanish names. The name was restored in 1973 as the team returned to the first division one year after nearly relegating, under young manager José María Maguregui.

Racing de Santander was immediately relegated, going on to spend the following years again bouncing between divisions one and two, also being crowned champions in Segunda División B (the new third level, created in 1977) in 1991. Veteran Quique Setién returned to his main club the following year, helping it return to the top flight and scoring in the 1994–95 campaign against FC Barcelona, in a historic 5–0 home win.

In the 2000s Racing only played one season in the second division, winning promotion with Setién as manager. In 2007–08, under Marcelino García Toral, it finished in sixth position, thus qualifying to the UEFA Cup for the first time ever; additionally the club reached the semifinals of the Copa del Rey twice during this decade, being ousted by eventual runners-up Getafe CF and Atlético Madrid in 2008 and 2010, respectively.