At the end of the season, three more Argentine players were signed: Juan Montes, Oscar Alvarez[11] 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.

[7] 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.

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

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.

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

[7] 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.

[33] 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.

In the semifinals, 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 formation.

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.

However, lack of defensive stability, poor tactics and serious goalkeeper errors, PAS suffered shocking loses against Panseraikos, Volos, Lamia and Kifisia.

Eventually, after a 13 games winless streak, Staikos resigned, becoming the first manager in 10 years to be replaced mid-season.After an awful season PAS Giannina finished on 14th and relegated to Super League Greece 2.

During the 2016–17 season, PAS Giannina competed on the UEFA Europa League qualifying rounds for the first time in the club's history.

PAS Giannina captain Alexios Michail opened the score from inside the box after a corner kick taken by Noé Acosta on the 7th minute.

PAS Giannina had total control of the game, and in the 31st minute Fonsi Nadales doubled his team lead with a great volley after a perfectly executed cross by Nikos Karanikas.

On the second half, the goalkeeper Alexandros Paschalakis with a presice volley across the whole length of the pitch, spotted Dimitrios Ferfelis who took advantage of the opposition's defenders error and sprinted towards goal with Acosta trailing.

However, the Epirus side managed to score after a remarkable dribble fooling the opposition defenders from Christopher Maboulou†, who let the ball pass beside him after a pass from Karanikas, to reach Leonardo Koutris who beat the goalkeeper, and formed the final score of 3–1 after extra time, and eventually led PAS Giannina to the Third qualifying round for the first time in the club's history.

The identity of the club is highly intense throughout the hole stamium, making PAS Giannina one of the most difficult and challenging opponents for everyone to beat.

On January 31, 2007, PAS clinched a spot in the Greek Cup semifinals by virtue of an extra-time goal from Evangelos Kontogoulidis before a hostile crowd in Karaiskakis Stadium.

With an aggregate score of 3–2, PAS Giannina also is the first ever lower division club that eliminated Olympiacos from the Greek Cup tournament.

The most famous player to have donned the blue and white PAS Giannina's jersey in recent years is defender Giourkas Seitaridis, who later played for Panathinaikos, FC Porto, Dynamo Moscow, and Atlético Madrid as well as the triumphant Euro 2004 Greece squad.

[51] There were fan clubs in Athens like Los Toros Locos (2001–2009) or Thessaloniki (Blue Vayeros Salonica (2006–2011).

In contrast, derby matches against AEL are competitive in the sporting sense but do not evoke the same feelings of enmity from PAS Giannina supporters.

[54] This rivalry has been increased since the summer of 2016, when Panionios was not granted a license by UEFA to compete in the Europa League following a claim by PAS Giannina.

UEFA ruled that PAS Giannina take Panionios’ place in the 2016 2nd qualifying round of the Europa League.

Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.