The club was founded on June 23, 1928. The club's inaugural President was Ramon del Hierro. The club did however have to cease operations in 1936 because of the Spanish civil war. Thereafter, they remained unactive until they formed on the 4th of September in 1946.
Leganes was a team that spent the bulk of its existence in lower leagues. In 1977, the club won the promotion up to fourth division which it had previously played for seven years while it was still a third division.
Following a steady growth, Leganes reached the new division three in 1987before moving into the 2nd division six years after, and keeping its league status for 11 seasons. In the same period, it earned two consecutive eighth-places (best) between 1995 and 1997.
On the 24th of December, 2008. Victoria Pavon and Felipe Moreno purchased a majority stake within the Club. From July of 2009 on, Victoria Pavon has been the president of the club.
For the season 2013-14, Leganes was promoted into Segunda Division after 10 seasons in Segunda B.
In the 2015-16 season as the only time they've ever done so Leganes were promoted into La Liga, which was completed on June 4, 2016 by the 1-0 victory away in a match against CD Mirandes, thus becoming the fifth team from the Community of Madrid to ever participate at La Liga after Real Madrid, Atletico Madrid, Rayo Vallecano which was sealed on 4 June 2016 after Rayo Vallecano, Atletico Madrid Getafe. They continued to play in the top division for four seasons, achieving the 13th spot in the 2018-19 season, only to be relegated in the final game of the season which was a draw at home in the final game against Real Madrid. The team was able to advance for the first time in semi-finals at the Copa del Rey, by defeating Real Madrid in the quarterfinals with a 2-1 victory at the Santiago Bernabeu Stadium.