Castillo, Benidorm, Córdoba, and Ecija fight for a spot in the 2nd division

In the 2005-06 season, SD Huesca brushed its fall to the 3rd Division. After a bad league campaign –in a year in which, on the other hand, the team finished runner-up in the Federation Cup after falling in the final against Puertollano–, they were forced to play the relegation phase against Castillo CF from the Canary Islands. After drawing at El Alcoraz, in the second leg in San Bartolomé de Tirajana, the 1-0 for the locals condemned the Huesca team to relegation for sixty minutes until a goal from Sestelo certified the permanence.

It was the beginning of the most brilliant era of SD Huesca. In the summer of 2006, the project of the club's Veterans Association, headed by José Antonio Martín, Petón, took over the reins of the entity –with Armando Borraz in the presidency– applying a new management model that seeks the professionalization of the club structures. The squad was almost completely renewed - betting on the sporting and human quality of a good part of the Aragonese football strongholds - and the changes quickly bear fruit.

In the 2006-07 season, qualification for the promotion phase to the 2nd Division was achieved for the first time. It is achieved in an agonizing way on the last day of the regular league in the match against Benidorm. In the final minutes, goalkeeper Rubén Falcón commits a penalty and is sent off. The young Huesca goalkeeper Jorge Larrosa –currently responsible for the maintenance of the El Alcoraz lawn– goes out cold on the field and stops the penalty that gives his team access to the league. In the first phase, Palencia is eliminated, but in the final tie, the powerful Córdoba asserted the 2-0 of the first leg, drawing 1 at El Alcoraz against almost 7,000 fans, and left SD Huesca at the gates of the 2nd Division in the brightest season in its 47-year history.

The goal came true just a year later. The team, with Onésimo Sánchez on the bench, once again finished 2nd in the regular competition and eliminated Gavá in the promotion before facing Écija. They won 2-0 at El Alcoraz in the first leg and in the second leg SD Huesca stoically resists in the second half the goal of the Andalusian international Nolito and the expulsion of his defense Dorado, thanks to a historic goal by Roberto in the minute 94, certify the first promotion of SD Huesca to 2nd Division. It was June 15, 2008.

The debut in the 2nd Division - 56 years after UD Huesca's debut - was notable, with a 2008-09 season that saw the team led by Antonio Calderón finish in 11th place. Canarian Rubén Castro, who would later play for the Spanish national team, scored SD Huesca's first goal in the 2nd Division in the competition's opening game, at home against CD Castellón (2-2). Particularly memorable was the first derby of Aragón in the 2nd Division since the creation of Huesca SD. It was on 6 December 2008 at the La Romareda stadium, with more than 5,000 Huesca fans shaking the stands thanks to the temporary 0-2 scoreline, from which Real Zaragoza managed to claw its way back in the last few minutes to secure the draw.

In its second season in the division, the team went through a couple of rough patches during the year, which complicated its continued presence in the division, embodied in a dramatic penultimate match in El Alcoraz against Cádiz (2-1, with goals from Helguera and Camacho) and certified in the last match in Vigo with a goal from Mikel Rico (0-1). In the 2010-11 season, the team assured its continuation through its defensive strength, symbolised by the 2nd Division's Zamora Trophy for fewest goals allowed, awarded to goalkeeper Andrés Fernández. In its fourth season in 2nd, after a complicated start that put SD Huesca in a relegation spot, the team posted a notable second half to the season, thus assuring its permanence.

It was in its fifth consecutive season in the 2nd Division that SD Huesca failed to secure its continued presence in the category. The team went through four coaches during the season and was unable to win in the last match against Recreativo de Huelva in the Estadio Colombino, which would have secured its place in the 2nd Division. The final 0-0 on that fateful afternoon doomed SD Huesca to the 2nd Division B of Spanish football.