Three years later, it visited the national categories for the second time; in 1962–63 it appeared in the playoffs for promotion to Segunda División, facing CF Badalona: amidst accusations of a fixed result, the club did not appear for their following match at SD Ponferradina, and eventually disappeared from the footballing maps.

On 17 June 1979, with another legendary Real Madrid figure as coach, Francisco Gento, Palencia was first promoted to second level after a 1–0 home win against Pontevedra CF, incidentally one day before the 50th anniversary of the first football match in the club's history – it lasted two seasons in this first tenure.

In 1982–83, right after the FIFA World Cup on home soil, the club produced arguably its best season, finishing fifth just three points shy of an historical La Liga promotion; three years later it disappeared, again due to economic issues.

On 1 July 2012, Palencia was relegated to the fourth level by the Royal Spanish Football Federation, due to non-payment of wages to its players.

[1] On 4 December the club was disbanded after failing to raise enough financial funds to run it until the end of the season, having incurred in a €1,7 million net debt from past years.