Construction work on the temple began during the reign of Amenhotep III in the 14th century BC. Horemheb and Tutankhamun added columns, statues, and friezes, and Akhenaten had earlier obliterated his father's cartouches and installed a shrine to the Aten.

However, the only major expansion effort took place under Ramses II some 100 years after the first stones were put in place. Luxor is thus unique among the main Egyptian temple complexes in having only two pharaohs leave their mark on its architectural structure.

Each year, to ensure the flooding of the Nile that was necessary to national prosperity, the statues of Amun, Mut (goddess of war), and Khons (the moon god) were sailed down the river to Karnak for a great festival.

The temple fell into disrepair during the Late Period. Alexander the Great claimed to have undertaken major reconstruction work "to restore it to the glory of Amenhotep's times" in the 320s BC. During Rome's domination of Egypt it was converted into a centre for the Roman emperor cult.

By the time of the Arab conquest, the temple was largely buried underneath accumulated river silt, to the extent that the Mosque of Abu Haggag was built on top of it in the 13th century (much reworked since, but one of the minarets dates back to the original construction).