Panionios Gymnastikos Syllogos Smyrnis was first established in 1890 in the ancient city of Smyrna. Initially competing as the Orpheus Music and Sports Club, the team adopted its current name in 1898. Panionios have spent almost their entire existence in the top flight of Greek football. Today, the club is based in Nea Smyrni, a suburb of Athens.
During the 1990s, Panionios suffered severe financial problems, which led to decreased quality of performances on the field and the municipality of Nea Smyrni taking ownership of the club. With the threat of bankruptcy looming, shares were released back to private owners in 2001. In 2006, shipowner Constantinos Tsakiris became the majority shareholder.
The Greek Cup has been the main source of success for the team, with their first win coming in 1979, after beating AEK Athens 3-1 in the final. A second cup win followed in 1998. This time, Panionios overcame Panathinaikos to win the competition. They have finished as runners up a further four times. Other honours include an Athens Championship in 1951 and a Balkans Cup, won in 1971. The 1970-71 season also saw Panionios achieve their highest ever league finish, as they finished in 2nd place, behind AEK Athens.
Over the years, a number of talented Greek footballers have represented the team. These players include Thomas Mavros and Nikos Anastopoulos in the late 1970s, Dimitris Saravakos and Nikos Tsiantakis in the 1980s, Takis Fyssas in the 1990s and Alexandros Tziolis in the 2000s. All six players went on to play for the national team. Álvaro Recoba is amongst the club's best-known foreign imports.
Panionios play their home matches at the Nea Smyrni Stadium, also known as Panionios Stadium. The ground first opened in 1939 and was made into an all-seater stadium in 1998. It is currently able to hold a maximum of 11,700 supporters. The attendance record was set in 1974 for a match with Panathinaikos, which was seen by 20,950 spectators.