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On 9 September 2009, César Antonio Contreras and Miguel Antonio Castillo along with Pedro Antonio Contreras and with the support of the Sonsonate department (in particular the head of the department José Roberto Aquino) were able to re-activate Sonsonate from defunct status and begin their time in the modern era.

The club competed in the Tercera División for a few years, before winning promotion to the Segunda División in 2011, under the direction of Ricardo Andrés Navarro.

Despite strong club following and several finals appearances the club failed to win either the Segunda Division Apertura or Clausura title to achieve promotion in the Primera Division.

However, on the 12 July 2015, the club purchased the spot of recently promoted Real Destroyer meaning the club will participate in the Primera division for the first time in fifteen years (last time was 1999).

Despite several Championship winning managers coaching Sonsonate, Peruvian Agustin Castillo, Uruguayan Rubén da Silva and Salvadoran Juan Ramon Sanchez have been the only coaches to qualify Sonsonate to the post season final series, the club reached the semi-finals under Agustin Castillo and Ruben Da Silva, and Quarter final under Juan Ramon Sanchez, before each time being eliminated by Alianza F.C.