PAS experienced a fair degree of instability in these years. In 2002–03, PAS Giannina finished 14th. After the penalty of 90 points the club finished 16th and relegated. The penalty of 90 points imposed on it by the Greek football association (EPO) for financial reasons. There were a lot of financial problems in season 2003–04. The club finished 14th and qualified to playout with Ilisiakos. The club lost 3–1 and relegated in the Third division for the second time in its history. The club turned on a semi-professional status.
