[1] Aegyptocetus is known from the articulated holotype MSNTUP I-15459, an almost complete cranium, lower jaws (with teeth) and a partial postcranial skeleton (cervical and thoracic vertebrae and ribs).

It was collected in the Khashm el-Raqaba limestone quarry (28°30′N 31°48′E / 28.5°N 31.8°E / 28.5; 31.8, paleocoordinates 22°54′N 27°12′E / 22.9°N 27.2°E / 22.9; 27.2)[2] from the Gebel Hof Formation on the northern flank of Wadi Tarfa in the Eastern Desert of Egypt, dating to the late Mokattamian age of the middle Eocene, about 41 to 40 million years ago.

The specific name refers to Wadi Tarfa, the desert valley where the holotype was found.

Its thoracic vertebrae (T1–T8), however, had long neural spines which is a characteristic of the weight-bearing system of land-living mammals retained in protocetids, such as Rodhocetus and Qaisracetus, but absent in the more derived basilosaurids, such as Dorudon.

This suggests that Aegyptocetus, like other protocetids, was able to support its body on land and probably was semi-aquatic.