Katsouranis signed a four-year contract with Greek Super League club Panathinaikos, on 1 July 2009 on a fee of €3.5 million. He has stated that it's the team he supported since childhood. He scored his first goal against Sparta Prague in the Champions League. He scored his first league goal against Skoda Xanthi on the 2nd matchday of the 2009–10 season. Katsouranis scoring abilities were a key part of Panathinaikos' good run during the first half of the season, as the defensive midfielder scored 8 goals in just half a season. He ended the season with Panathinaikos managed to end the season positively by winning the double with the 2009–10 Greek Cup final against Aris Thessaloniki. Katsouranis ended his long wait for his first trophy by helping the Greens win the domestic double in his first season; was the team's second top scorer (behind Djibril Cissé) with eight goals in the Superleague Greece triumph.