The town became internationally famous in 1977, when the Greek archaeologist Manolis Andronikos unearthed the burial site of the kings of Macedon, including the tomb of Philip II, father of Alexander the Great. The finds established the site as the ancient Aigai.
On the lid of the larnax of Philip II there is a symbol of a sun or star and this Vergina Sun has been adopted as a symbol of Greek Macedonia. It became the subject of international controversy in 1991 when the newly independent Republic of Macedonia used the symbol on its flag. This outraged Greek public opinion, which saw the use of the symbol as an appropriation of Greece’s historical heritage and as implying a territorial claim on Greece. In 1995 the Republic of Macedonia agreed to change its flag.

Archaeologists were interested in the hills around Vergina as early as the 1850s, supposing that the site of Aigai was in the vicinity and knowing that the hills were burial mounds. Excavations began in 1861 under the French archaeologist Leon Heuzey, sponsored by the Emperor Napoleon III. Parts of a large building that was considered to be one of the palaces of Antigonus III Doson (263–221 BC), partly destroyed by fire, were discovered near Palatitsa, which preserved the memory of a palace in its modern name. However, the excavations had to be abandoned because of the risk of malaria. The excavator suggested that this was the site of the ancient city Valla, a view that prevailed until 1976. Recent excavations have dated the palace to the reign of Philip II.

In 1937, the University of Thessaloniki resumed the excavations. More ruins of the ancient palace were found, but the excavations were abandoned on the outbreak of war with Italy in 1940. After the war the excavations were resumed, and during the 1950s and 1960s the rest of the royal capital was uncoved including the theatre in which Philip II was murdered at the wedding of his daughter Cleopatra to King Alexander of Epirus.

The Greek archaeologist Manolis Andronikos became convinced that a hill called the Great Tumulus (Greek: Μεγάλη Τούμπα) concealed the tombs of the Macedonian kings. In 1977, Andronikos undertook a six-week dig at the Great Tumulus and found four buried chambers, which he identified as hitherto undisturbed tombs. Three more were found in 1980. Excavations continued through the 1980s and 1990s. Andronikos claimed that these were the burial sites of the kings of Macedon, including the tomb of Philip II, father of Alexander the Great (Tomb II). Andronikos maintained that another tomb (Tomb III) was of Alexander IV of Macedon, son of Alexander the Great and Roxana.

This view is challenged by some archaeologists. Studies by Eugene N. Borza, utilizing the construction of the ceilings of Tomb II, the incorporation of a weight measurement system introduced by Alexander the Great on golden objects in the tomb, Asian themes on the tomb’s friezes, and the discovery of a scepter similar to that found on coins minted under Alexander’s reign, as well as studies which utilized anthropological data, suggest that this tomb belongs to Alexander’s half-brother Philip III Arrhidaeus and his wife, Adea Eurydice. Instead, according to Borza, Tomb I, also known as the Tomb of Persephone, may have contained the remains of Phillip II and his family. If this theory is true, then the golden weaponry and royal objects found in Tomb II may have belonged to Alexander the Great.

On the other hand, 2010 research provided support for the argument that Tomb II could not have belonged to Philip III Arrhidaus and his wife. This research, based on detailed study of the skeletons, vindicates Andronikos and supports the evidence of facial asymmetry caused by a possible trauma of the cranium of the male, evidence that is consistent with the history of Philip II.[14] Moreover, further recent discoveries in the necropolis suggest an alternative site for Arrhidaios and Eurydike’s tomb, although details of this claim are yet to be revealed.

In March 2014, five more royal tombs were discovered in Vergina, possibly belonging to Alexander I of Macedon and his family or to the family of Cassander of Macedon.

The museum, which was inaugurated in 1993, was built in a way to protect the tombs, exhibit the artifacts and show the tumulus as it was before the excavations. Inside the museum there are four tombs and one small temple, the heroon built as the temple for the great tomb of Philip II of Macedon. The two most important graves were not sacked and contained the main treasures of the museum. Tomb II of Philip II, the father of Alexander was discovered in 1977 and was separated in two rooms. The main room included a marble sarcophagus, and in it was the larnax made of 24 carat gold and weighing 11 kilograms. Inside the golden larnax the bones of the dead were found and a golden wreath of 313 oak leaves and 68 acorns, weighing 717 grams. In the room were also found the golden and ivory panoply of the dead, the richly-carved burial bed on which he was laid and later burned and silver utensils for the funeral feast. In the antechamber, there was another sarcophagus with another smaller golden larnax containing the bones of a woman wrapped in a golden-purple cloth with a golden diadem decorated with flowers and enamel. There was one more partially destroyed by the fire burial bed and on it a golden wreath representing leaves and flowers of myrtle. Above the Doric order entrance of the tomb there is a wall painting measuring 5.60 metres which represents a hunting scene.

In 1978 another burial site (Tomb III) was also discovered near the tomb of Philip, which belongs to Alexander IV of Macedon son of Alexander the Great. It was slightly smaller than the previous and was also not sacked. It was also arranged in two parts, but only the main room contained a cremated body this time. On a stone pedestal was found a silver hydria which contained the bones and on it a golden oak wreath. There were also utensils and weaponry. A narrow frieze with a chariot race decorated the walls of the tomb.

The other two tombs were found to have been sacked. Tomb I or the Tomb of Persephone was discovered in 1977 and although it contained no valuable things found, on its walls was found a marvellous wall painting showing the abduction of Persephone by Hades. The other tomb, discovered in 1980, is heavily damaged and may have contained valuable treasures while it had an impressive entrance with four Doric columns. It was built in the 4th century BC and the archaeologists believe that the tomb belonged to Antigonus II Gonatas.