The club was founded on 11 September 1949 and started and continues to be based in the town of Santa Rosa de Lima in the department of La Union.

The club began playing in the second division and spent almost twenty years there until in 1971 Municipal Limeño got promoted to the top flight at the expense of UCA.

The club were forced to play a promotion-relegation battle against Once Municipal in which the team lost and were relegated to the second division along with Juventud Olímpico.

[3] On 26 June 2009, Chalatenango going through financial troubles, sold their spot in the top flight Primera División to side Limeño.

However their campaign was an unhappy one with them finishing second last and forcing them to play a promotion/relegation match against Once Municipal which they lost and were relegated to the Second Division and that's where the club has remained ever since.

[4] Municipal Limeno confirmed a fourth relegation from the Primera division on 2 May 2022 despite a 1–0 victory over Isidro Metapan at Jose Romero Berios.

[7] The club reached its first grand final in 24 years, after defeating Isidro Metapan and Platense, However the club experience was humiliating one, losing 5-0 against Alianza, with Emerson Mauricio scoring four goals (a record in a final) and Honduran Ever Alvarado being sent off on 21st minute, Limeno played the rest of the game with 10 men.

[8] Municipal Limeño plays their home matches on the Estadio Jose Ramon Flores in the suburb of Santa Rosa de Lima in La Union.

Limeno has supported a long rivalry with Pasaquina for geographical reasons, since both are from the province of La Union; this clash is called the "Derby Unionense."

Limeno's shirts have previously been sponsored by Tapachulteca (1988–1999), TACA (1992), Pepsi (1999), Diana (2007–2013), Pilsener (2007–2013), Burger King (2013) and Tigo (2009).

As of January 2025 Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.