In 1979, Greek football turned professional. The Vardinogiannis family purchased PAOs football department and Giorgos Vardinogiannis became president. Panathinaikos were one of the first Greek clubs that formed a womens team in 1980, but that department is currently inactive.The transformation period lasted a few years, but in 1982 the club won its first professional era trophy, the Greek Cup, and during the 1980s they would go on winning two championships (1984, 1986), four more Greek Cups (1984, 1986—with a 4–0 against Olympiacos in the final—, 1988, 1989) and the Greek Super Cup in 1988. 


The great star of the team during these years was Dimitris Saravakos, nicknamed The Kid. Saravakos, a high-technique explosive miedfielder and iconic captain of Panathinaikos, was the alsolute idol for the fans during the 1980s, while other players included Nikos Sarganis, Spiros Livathinos, Velimir Zajec, Juan Ramón Rocha, Christos Dimopoulos and Giannis Kyrastas.



In the 1984–85 season, Panathinaikos, with coach Jacek Gmoch and stars Dimitris Saravakos, Velimir Zajec, Juan Ramón Rocha and Ioannis Kyrastas, made a run in Europe, eliminating Feyenoord, Linfield and IFK Göteborg to reach the semi-finals of the European Cup, where they were knocked out by Liverpool.In 1987–88, they made it also to the quarter-finals of the UEFA Cup, eliminating Juventus, Auxerre and Budapest Honvéd. Dimitris Saravakos was top scorer of the competition.The 1990s were an even more successful period for the club, both nationally and internationally. Four Greek championships (1990, 1991, 1995, 1996), four Greek Cups (1991, 1993, 1994, 1995) and two Greek Super Cups (1993, 1994) were awarded to the club.In the 1991–92 season, Panathinaikos reached also the last eight of the European Cup and took part in the first ever European tournament to have a group stage.In 1995–96, with Juan Ramon Rocha as coach and key players Krzysztof Warzycha, Józef Wandzik, Stratos Apostolakis, Georgios Georgiadis, Dimitris Markos, Giannis Kalitzakis, Giorgos Donis and Juan Jose Borrelli, Panathinaikos reached the Champions League semi-finals, finishing first in the group stage against Nantes, Porto, Aalborg BK and eliminating Legia Warsaw in the quarter-finals.In the semi-finals, Panathinaikos faced Ajax, recording an impressive 0–1 first leg away victory with Krzysztof Warzycha scoring the winning goal. Ajax had a record of 22 undefeated international matches until then, with Panathinaikos breaking their series. The Greek team, however, suffered a 0–3 defeat on the second leg. Thus, Panathinaikos was denied entry to a Champions League final once more.


In the summer of 2000, President Giorgos Vardinogiannis resigned from his duties with complaints for the refereeing situation in Greece and passed his shares to his nephew Giannis Vardinogiannis, who changed the style of the clubs management. Angelos Anastasiadis was initially appointed coach of the team and later the ex-player Giannis Kyrastas.With the arrival of coach Sergio Markarian, Panathinaikos reached the quarter-finals of the 2001–02 UEFA Champions League, being eliminated by Barcelona. Panathinaikos had passed the first group stage as the top club against Arsenal, Mallorca and Schalke 04, and the second group stage as second against Real Madrid, Porto and Sparta Prague.In the first leg of the quarter-finals, Panathinaikos managed to defeat Barcelona by 1–0 in Apostolos Nikolaidis Stadium. The second leg in Camp Nou was to be an eventful one. Panathinaikos scored first thanks to a beautiful goal by Michalis Konstantinou but eventually was eliminated as Barcelona scored three goals.

Ιn Europe, Panathinaikos made it to the quarter-finals of UEFA Cup quarter-finals. En route, the Greek team had knocked-out Litex Lovech, Fenerbahçe (with an impressive 4–1 win in Apostolos Nikolaidis Stadium), Slovan Liberec and Anderlecht. During the quarter-finals, although winning the first match in Estádio das Antas against eventual winners of the trophy FC Porto of José Mourinho, with the header of Emmanuel Olisadebe, they were eliminated in the second leg after extra time.




Notable players of this team included Takis Fyssas, Giorgos Karagounis, Antonis Nikopolidis, Angelos Basinas, Nikos Lyberopoulos, Michalis Konstantinou, Giourkas Seitaridis, Sotirios Kyrgiakos, Paulo Sousa, Goran Vlaović, Rene Henriksen, Joonas Kolkka, Jan Michaelsen and Emmanuel Olisadebe, considered by the fans one of the best teams in the clubs history.During 2002–03 Alpha Ethniki season, they lost the Greek championship in the last two games by arch-rivals Olympiacos. Under the guidance of Israeli coach Itzhak Shum, Panathinaikos managed to win the championship in 2004.They won also the Cup, beating Olympiacos 3–1 in the final, making the double. New players like Ezequiel González, Lucian Sanmartean and Markus Münch had signed the summer before. In the Champions League, they came third in the group stage facing Manchester United, VfB Stuttgart and Rangers.However, Shum was unexpectedly fired early in the next season (2004–05) and Zdeněk Ščasný succeeded him on the bench. Panathinaikos finished second in the championship, while in the Champions League they came again third in the group stage facing Rosenborg, PSV and Arsenal. They continued in the UEFA Cup, where they were eliminated by Sevilla.In 2005, major changes were made in the teams roster. Players like Angelos Basinas and Michalis Konstantinou departed, while others like Flávio Conceição, Igor Bišćan and Andreas Ivanschitz arrived. Ščasný gave his seat to Alberto Malesani. At the start of the 2006–07 season, Malesani left the team and was replaced by Hans Backe, who left only three months after his appointment; Víctor Muñoz was his replacement. For the 2007–08 season, Panathinaikos hired José Peseiro.On 22 April 2008, and under pressure from the fan base, main shareholder Giannis Vardinogiannis gave a press conference in which he announced the decision of his family to reduce their share in the club to 50%—after 30 years of full ownership—through an €80 million increase of the companys capital stock. After the negotiations and the share capital increase, the Vardinogiannis family would hold 56% of the club, the amateur Club 10% and the other shareholders 34% (with main investors Andreas Vgenopoulos, Pavlos Giannakopoulos, Adamantios Polemis and Nikos Pateras). Nikos Pateras was selected to be the new president of the club.

Djibril Cissé, two seasons in row top scorer for the Greek leagueFollowing the major changes in 2008, Panathinaikos hired Henk ten Cate as coach and bought many expensive players, such as Gilberto Silva from Arsenal and Gabriel from Fluminense. In the 2008–09 season, the Greens proved that they could hold their weight in the Champions League by reaching the last 16. However, they disappointed in the Greek Championship, finishing third in the regular season, though they managed to come second overall after the playoff mini-league.

The 2009–10 season was a successful one for Panathinaikos. During the summer transfer period, the club bought Djibril Cissé from Marseille, Kostas Katsouranis from Benfica, Sebastián Leto from Liverpool and various other players, spending more than €35 million in total. Henk ten Cate left in December to be replaced by Nikos Nioplias. The team managed to reach the last 16 of the Europa League, eliminating A.S. Roma after two amazing matches in Olympic Stadium of Athens and Stadio Olimpico. Panathinaikos also won both the Greek Championship and the Greek Cup, beating Aris by 1–0 in the final of the latter, thanks to a goal by Sebastián LetoIn 2011, due to financial problems and management disagreements, Panathinaikos sold Cissé for €5.8 million to Lazio and first-choice goalkeeper Alexandros Tzorvas to Palermo in order to reduce the budget.

New players then entered, such as Quincy Owusu-Abeyie, Toché, Vitolo and Zeca. The club also changed their president and chose Dimitris Gontikas to be the new chairman. Panathinaikos failed to qualify to the group stage of 2011–12 Champions League after they were knocked out by Odense BK 4–5 on aggregate.