The Palace of Phaistos with its superb architectural composition and its almost perfect construction, is considered to be the finest and most typical of all Minoan palaces. The ruins of the old and new palace are preserved today, the former having been protected under a shed. The nucleus of the new palace is a central peristyle court around which the rooms are arranged: the storerooms and shrines on the west side, the royal quarters on the north and the workshops on the east. To the west of the storerooms is the "theatral area" with the "processional ways" and, in the lower strata, the granaries of the Old Palace period (first palace). The West Propylon, the monumental entrance to the palace is the most impressive known structure of its kind. The finds from the palace are now exhibited in the Archaeological Museum of Herakleion.

Like at Knossos, the first (old) palace was built at the beginning of the 2nd millenium B.C. (MM I period) and remained in use for about three centuries (2000-1700 B.C.). It was destroyed by fire in ca. 1700 B.C. On its ruins a new palace was erected but was also destroyed in the mid-15th century B.C. (LM IB) along with the other Minoan palatial centres. The palace was abandoned thereafter and only some of its parts were occupied by individuals in the late Post-palatial period. In the Archaic period the temple of the Great Mother or Rhea was built on the remains of the Old Palace period, in the southern part of the palace.