On 10 September 2009, the last day of the Greek transfer period for free agent players, Seitaridis signed a 4-year deal with Panathinaikos, returning to the team after five years. It soon became apparent that Giourkas was unfit and was struggling to re-establish himself due to frequent injuries, missing most of the 2009–10 season's matches. However, on 21 March 2010, he surprisingly returned to the line-up for the big derby against rivals Olympiacos, and despite their defeat, Panathinaikos managed to end the season positively by winning the double. Seitaridis himself didn't appear at the 2009–10 Greek Cup final against Aris Thessaloniki due to injury, but made 2 appearances on the road to the final.