The mortuary temple of Merenptah is situated on the right-hand side of the necropolis road, just north of the Antiquities Inspectorate and next to the Marsam Hotel.

Merenptah was the son and successor of Rameses II. His temple has long been destroyed, probably due to its position close to the Nile flood plain and the rising water which also destroyed the temple of Amenhotep III. Merenptah used many blocks from Amenhotep's temple and from other nearby temples in the construction of his own monument. Petrie first examined the site in the 1890s, uncovering many of the earlier blocks and in the last two decades of the 20th century the Swiss Institute of Archaeology with the support of the Egyptian Supreme Council for Antiquities have been working on the site excavating and restoring the remains.

The structure was fairly typical of a late New Kingdom funerary temple. It was similar in plan to that of Merenptah's grandfather Seti I, at Qurna, and copied much of the design from his father's mortuary temple, the Ramesseum. There were two pylons and courts and it seems that the original building was changed and enlarged replacing the mudbrick pylons with stone and adding statues of the living king to its pillars. In the first court a huge stela of Amenhotep III was found which had inscribed texts by Merenptah on the reverse side telling of his victories in the Libyan War. This information, from Merenptah's year 5, includes the earliest historical reference to Israel and is known as the 'Israel Stela', now in Cairo Museum.

The second pylon was on higher ground on the gently sloping desert between the flood plain and modern village of Qurnet Murai. The second court had three porticos with Osirid pillars. The western portico formed part of the façade of the temple with two hypostyle halls, the first with twelve columns and the second with eight. From this, there were side chambers, the sanctuary area and barque shrines for the Theban Triad of Amun, Mut and Khons. A chapel of Osiris was to the south and a sun-court with a large altar to the north, similar to that in the Temple of Seti I. A slaughterhouse was attached to the north-western corner of the building.

Southern subsidiary buildings were additions and included a priest's house, the temple well and a complex of workshops. The temple was surrounded by mud-brick buildings including a small palace adjoining the southern wall and rows of brick magazines and storerooms. A miniature sacred lake can still be seen within the temple precinct.

The Temple of Merenptah has now been opened as a museum. Many well-preserved blocks and wall fragments containing colourful reliefs of Amenhotep III are displayed, alongside stonework from other monuments on plinths inside the temple complex. Much of it has been re-carved for Merenptah. Many fine examples of statuary and architectural fragments can be seen in the museum's magazines including a part of a colossal limestone sphinx and jackal-headed sphinxes. A purpose-built museum houses many artefacts found on the site and gives a history of the restoration.