At the end of the season, three more Argentine players were signed: Juan Montes, Oscar Alvarez[7] and Eduardo Lisa.

The club finished several times near the top of the First Division table, often earning victories over more established Greek teams such as Olympiacos, Panathinaikos, AEK Athens and PAOK.

The effective and spirited play of the club during these years drew flattering comparisons with the famous Dutch club Ajax Amsterdam, and the moniker "Ajax of Epirus" has stuck with the team ever since.

[3] In the middle of the season, former Poland national team coach Jacek Gmoch was signed from the Epirote club.

The period following the aforementioned peak years of the club generally marked a sharp decline in the fortunes of it as many of its top stars moved on or retired outright without being satisfactorily replaced.

[3] The club qualified for the promotion playoffs with Ethnikos Piraeus, Apollon Kalamarias, Korinthos, Diagoras and Veroia.

The penalty of 90 points imposed on it by the Greek football association (EPO) for financial reasons.

[3] Also, PAS Giannina reached the semi-finals of the Greek Cup 2006–07 against AE Larissa FC.

On the quarter-final PAS Giannina won Olympiacos, 2–0 at home and lost 2–1 in Karaiskakis Stadium of an extra-time goal from Evangelos Kontogoulidis before a hostile crowd.

In the summer of 2008, ownership of the club was passed over to Giorgos Christovasilis, a businessman from Athens whose roots are from the Epirus region.

He signed Guillermo Ángel Hoyos as manager[20] and some great players such as Luciano.

In the summer of 2009, the club signed players such as Dimitrios Eleftheropoulos, Ibrahima Bakayoko, Konstantinos Mendrinos, Ilias Kotsios.

[3] In 2012–13, PAS Giannina finished 5th and qualified for the playoffs with Atromitos, Asteras Tripolis and PAOK for the first time in its history.Also, Giannis Christopoulos won the best manager of the year award.

[28] The club qualified for European competitions, except Balkans Cup, for the first time in its history.

An important moment was the charity match for the refugees between the veterans of the club and FC Barcelona.

[29] The charity match and activities were organized by the Barça Players Association in collaboration with the United Nations High Commissioner for Refugees (UNHCR) and with the support of PAS Giannina FC.

[31] In 2018–19, after an awful season, PAS Giannina finished 14th and relegated to the Super League 2.

Petrakis left the club after years and a new manager, Argiris Giannikis was hired.

The team got into the semi-final of the Greek Cup in the season 2020–21 after beating Atromitos and Panathinaikos.

In the semi-finals, the club lost from Olympiacos on aggregate 2–4, the only team considered capable to beat the in-form PAS Giannina side at the time by the Greek fans, many of whom considered the Epirus side the favorite to win in the final against either AEK or PAOK if qualified.

The team consisted mainly of debutant players who were performing at their best such as Alexandros Kartalis, Christos Eleftheriadis, Nicolae Milinceanu etc.

This was one of the clubs most successful campaigns mostly due to the defensive style of play used by the coach Iraklis Metaxas, using the containing 4-4-2 double six.

Rock solid defence was a result of great chemistry, athleticism, leadership, playing abilities and great passion from the goalkeeper, Yuri Lodygin who is regarded as the best goalkeeper to ever play for the Epirus side, and the defenders Peersman, Erramuspe, Kargas and Saliakas.

On the midfield, PAS Giannina signing from Super League 2 club Levadiakos, Zisis Karachalios completed one of the best seasons of his career, alongside Domínguez for the first half of the season, and Caleb Stanko for the second half.

Karachalios provided great support in defence, helping the team with his very high work rate, stamina, strength, interceptions and steals, being ranked as the player with the most steals in Super League 1.

[37] Perea made a great season scoring 10 goals helping PAS Giannina on attack.

[38] After the season 2021–22 the club start to change skin, the goalkeeper Yuri Lodygin moved to Panathinaikos[39] and also players like Michael Gardawski, Antonis Ikonomopoulos, Marvin Peersman, Giannis Kargas, Jan-Marc Schneider, Fabricio Brener and Stefanos Siontis have been realized.