During the first years of the Copa Perú the six regional champions played a round robin tournament in Lima in which the team with the most points was promoted to the Peruvian Primera División.

Because only points and not goals were taken into consideration, a play-off game was played on neutral ground in Lima where Sport Áncash lost 3–1.

In 2004 under the leadership of José Mallqui as president and Tito Chumpitaz as coach,[Web 3] Sport Áncash would win the Copa Perú and make it to the Peruvian Primera División for the first time.

In the finals, they defeated one of the oldest teams in the country, Deportivo Municipal, who had qualified as the 2004 Peruvian Segunda División runner up.

They should have been relegated anyway because of inscription problem with their squad members were it not for a questionable amnesty granted by the Peruvian Football Federation.

Over all it finished 3rd in the league which qualified it for the first international tournament in its history, the 2008 Copa Sudamericana alongside Universitario de Deportes.

With the help of Antonio Alzamendi, Sport Áncash was able to fight for the Torneo Clausura and finish 3rd and 6th in the aggregated table only staying away from another international tournament by goal difference.

In 2009 the club was not able to save itself from relegation by finishing 15th in the new 16 teams tournament only one point away from the 14th place occupied by Alianza Atletico.

José Mallqui was joined by Reynaldo Huayaney in an effort to control the massive amount of debt that the club carried over from its bad year in the Torneo Descentralizado.

During their first season in the Peruvian Segunda División, Sport Áncash tied on points with Academia Cantolao from Callao and forced a title play-off match which they lost 2–0.

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