The Philae Temple complex includes many buildings dating back to the Ptolemaic period (332-30 BC), the most notable of which is the temple begun by Ptolemy II Philadelphus (285–246 BC), dedicated to Isis, the mother of Horus, the god of kingship. One of the notable scenes is in the Mammisi or Birth Chamber, where the birth of Horus was celebrated, showing Isis breastfeeding her son Horus in the reeds.

The Temple of Isis is considered one of the most enduring ancient Egyptian temples, as it continued to function until the reign of the Byzantine Emperor Justinian I (527–565 AD), who ordered the closure of all pagan temples. A priest named Ismet-Akhom engraved the last hieroglyphic inscription, dating back to the 4th century AD (394 AD). The temple was converted into a church, and many of the temple's inscriptions were erased.

Next to the Temple of Isis is a temple dedicated to Hathor, built by Ptolemy VI Philometor (180–145 BC) and Augustus, the first Emperor of Rome (30 BC–14 AD). The Trajan's Kiosk (98–117 AD) located in front of the Philae Temple still stands, though its roof is no longer present. The regular arrangement of its magnificent columns attracted the attention of travelers, who described and photographed it. Isis was the main deity of the area, and emperors were depicted offering sacrifices to her, her husband Osiris, and their son Horus.

All these monuments were relocated from the original Philae Island to the nearby Agilkia Island during the UNESCO Nubian Campaign in the 1960s to save the sites submerged by the Nile waters due to the construction of the Aswan High Dam.