Gondomar's early foundations were established on 1 August 1928, as the club registered in the Porto Football Association.

In 1932, however, it ceased all activity, until a group of people dubbed Os Teimosos de Gondomar (Stubborn), ten years later, took it upon themselves to resurrect the club, which return to organized football in 1960, in the third regional division; promotion to the second regional level was achieved five years later.

On 27 October 1986, the team participated for the first time in the Portuguese Cup, losing 1–2 at F.C.

In 2003, whilst competing in the third division, it made nationwide headlines after eliminating Benfica in the fourth round, with a 1–0 win at the Estádio da Luz.

In the 2006–07 season, the club achieved its best-ever classification in the category, finishing fifth.