AD Isidro Metapan

In 2000, Metapán FC and Isidro Menéndez, two Second Division strugglers, chose to merge. In 2001, the newly born club won promotion to the Primera División with a 3–2 playoff win over Jocoro FC.

The club quickly consolidated their position as a mid-table side, and starting in Apertura 2004 began making title pushes. They qualified for the playoffs for the first time that year by defeating Luis Ángel Firpo in a fourth place playoff. In Apertura 2005, they finished the regular atop the table, defeated Once Municipal in the semi-finals, and only fell short of their first title after a 2–0 extra time loss to Vista Hermosa.

In Clausura 2007, the club finally bettered that result, taking home their first ever championship with a 1–0 extra time win over Luis Ángel Firpo. That qualified the team for the CONCACAF Champions League for the very first time, although they did not get past the preliminary rounds.

Over the next several years, Isidro Metapán began to surpass the traditional powers of Salvadoran football (FAS, Firpo, Alianza, and Águila). They won their second title in a penalty shootout over Chalatenango in Apertura 2008, then defended their crown in Clausura 2009 with a 1–0 win over Luis Ángel Firpo. Alexander Amaya scored the winner in the 58th minute.

After a near miss in the Apertura 2009, Isidro returned to the top for the third time in four seasons by winning the championship of Clausura 2010. Léster Blanco and Paolo Suárez each scored in a 3–2 win over Águila. In each season from 2007 to 2010, the club had won the title at least once. They would win it for a fourth time in five in Apertura 2010, beating Alianza 4–3 in a penalty shootout.

2011–2012 was the most successful season in club history. It started in the summer, in the CONCACAF Champions League. Metapan qualified for the group stages, and a 2–0 win over Mexican team Santos Laguna allowed them to qualify out of the groups into the quarterfinals for the first time. Although UNAM Pumas eliminated them at that stage, it had still been a very successful run.

Meanwhile, domestically, Metapán won a sixth title in eight years with a 1–0 victory over Once Municipal the only goal coming from Paolo Suárez in the 51st minute.

They narrowly missed a repeat that spring in the Clausura, losing 2–1 to Áquila in the championship match. However, they recovered to win a seventh championship in nine years, defeating Alianza in extra time to win the Apertura 2012. For a moment it looked like the hero would be Metapán's top goal scorer Nicolás Muñoz, who scored from a free kick in extra time. However Sean Fraser of Alianza equalized with a header, forcing the match into penalties. After a dramatic shootout, Isidro Metapán won 6–5.

They won their 8th title in Apertura 2013, beating FAS 1–0 on a goal from Andrés Flores in the 85th minute.

On 25 May 2014 Isidro Metapán won the Primera División title for the ninth time in the club history, defeating Dragón on penalties 6–5.

Title number 10 came in Apertura 2014, as Metapán defeated Águila in penalties 3–2. Once again, Nicolás Muñoz played a very important role in taking the match to penalties with an extra time goal.