It is a historic municipality, which has been inhabited since prehistoric times. In 3200 B.C., the hamlet of Askitarios was built on the homonymous small rocky peninsula south of the site where Marikes Beach is today. The settlement enjoyed prosperity - adorned with small rectangular stone homes, blooming flora coverages, a central fire,  cobblestone path divisions, a cemetery in the south,  and a Protohelladic Acropolis.

Excavations in Askitarios took place from 1952 - 1954, by Dimitrios Theocharis. The word "Askitario" later came from a cave that a monk from the Penteli Monastery had turned into a retreat. North of the Rafina stream between the main harbor, bronze treatment facilities were unearthed.

Askitarios had begun to decline since the beginning of the first millennium, then the settlement of Rafina (or Arapinos) was created in the place where the main port is today. Rafina was one of the 100 municipalities in Athens that Cleisthenes appointed, named Arafin. This name was taken by its first governor, Arafina, who was one of the 100 heroes of Attica.
 

Excavations in the area also found evidence from the Roman Period. Moreover, during the Asia Minor Catastrophe of 1922, many residents of Triglia of Asia Minor arrived in Rafina, most of them with ships of the Triglian shipowner, Philippos Kavounidis. They settled in Rafina and formed a refugee settlement called Nea Triglia, but it did not prevail. There is a museum that has been preserved since that time. It belonged to a family that came to Rafina following the disaster and is the only one that has survived to this day. It includes all of the furniture and equipment of the family that inhabited the premises.

The refugees further built the Holy Church of the Assumption of the Virgin Mary in the center of the city. In 1929 building was completed but without any of the original icons from the churches of Triglia. Those that had been protected by the Turks went to the Byzantine Museum of Athens, who initially refused to surrender them because some icons (such as the Holy Visit) were of great value. Eventually, after many attempts, the refugees managed to recover them. The chapel of Aghios Fanourios, which was erected next door, was the church's Holy Tomb. In the 1950s, the old town of Rafina was almost completely demolished in order to build the modern city.

Concurrently, the first church of the Assumption of Virgin Mary of Pantavassilissi was demolished and only the chapel of Agios Fanourios was preserved. Today the national telephone company 'OTE Rafina' is found in the place of the first church. The second church of the Assumption of the Virgin Mary, which we see today next to the central square, was raised very close to the first. The work was completed in 1958 and is considered the patron saint of the city.