After a ten-year spell in the top flight, encompassing 12 seasons in the 1970s/80s, the club only returned again in the 1996–97 campaign: though eventually relegated it managed two remarkable comeback wins over FC Barcelona, which ultimately handed the league title to Real Madrid.
In 2004–05, after five years in the third level, Hércules finished second, being subsequently promoted to the "silver category". After posting three consecutive solid seasons, the club narrowly missed out on a return to the top division in 2009, finishing fourth three points behind last-promotee CD Tenerife.
The 2009–10 campaign saw Hércules promoted back into the top flight after 13 years, in dramatic fashion: losing 0–1 at half-time at Rayo Vallecano, the team fought back to win 2–1 in the penultimate game of the season and leap frog Real Betis into third place. In the last round, a 2–0 away win against relegation-threatened Real Unión guaranteed promotion, with the 4–0 win of Betis over Levante UD eventually counting for nothing (all three teams – Levante, Hércules and Betis – ended with the same number of points).
Early into the 2010–11 season, one year, three months and 19 days after Barcelona's last home defeat in the league, Hércules recorded a shock 2–0 win at the Camp Nou, thanks to a brace from Nelson Valdez –Barça had won their last 11 home matches, scored at least three times in each of their last six league fixtures and were protecting a 17-game unbeaten streak. Amazingly, however, this was the Alicante outfit's third successive win over the Catalans, having won both meetings in their previous top flight campaign 14 years before; after a solid first round of 19 games the team slumped in the table, eventually ranking in 19th position for an immediate relegation back.