Their foundation was the result of the love of the football-loving world of Giannitsa, who wanted a strong team, present in football events.

Between the years 1950 and 1951, there was a lot of football activity in the local community, with the establishment of four clubs that were the forerunners of the current group.

In 1955, a process of merging the local teams began, resulting in the emergence of two dominant clubs by 1960, Makedonikos Giannitsa and Pontiaki Neola.

Finally, in 1961, Macedonikos Giannitsa and Pontiac Youth merged, resulting in the creation of Anagennisi Giannirsa.

They started playing in the local league of Central Macedonia and made their first appearance in the second national division in the 1964–65 season, winning the 1st place in the 4th group, which is the highest ranking in their history so far.

They did not manage to get the promotion to the first national division, as in the final phase they finished in the third place among the winning teams of each group.

In the institution of the Greek Cup, Anagennisi Giannitsa do not have to demonstrate any particular success, as they has never progressed at least to the quarter-final phase of any competition.