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UNAN Managua has spent much of its history struggling to earn promotion to the top flight. Their first serious effort came in 2008–2009, when they earned their way into a relegation playoff against Real Madriz. They lost, 7–2 on aggregate. In 2011–2012, UNAN Managua won the Clausura and earned a promotion playoff with Apertura champion Xilotepelt. Once again, they lost.

However, in 2013–2014, UNAN won the Apertura 2013 title. The Clausura that year was won by Real Esteli's feeder side, which was not eligible for promotion, and so UNAN automatically moved up into the top flight. Their first season, 2014–2015, was a struggle. The club won just eight of 36 top flight matches and was forced into a promotion/relegation playoff with San Marcos. They won, 6–0 on aggregate, but were still not expected to have much of an impact on the table in 2015–2016.

Instead, they stunned Nicaragua by storming to a 3rd-place finish in Apertura 2015, good enough for their first playoff berth. Then, in the postseason, they defeated Walter Ferretti and Diriangén to claim their first national crown. It ended a decade of dominance for Ferretti, Diriangén, and Real Esteli. Although Managua lost the season championship to Clausura winners Real Esteli, their championship was nonetheless a special one.

They spent the next two years as a regular playoff participant, then staved off relegation in 2017–2018.