Qena has undergone many name changes in its long history. During the Pharaonic era it was known as Shabt, then under Greek rule it was known as Quijulis.  When the Romans took control, they named it Maximyat, while during the Coptic era it was known as Qona Okona. Finally, after the Islamic conquest, it was renamed Aqny, from which its current name is derived.

The River Nile mediates the governorate, which contributes to agricultural activity. The Red Sea mountain chains are located to the east, and the Western Desert is in the west. Because of the many granite outcrops in this region, the river changes its course in Qena, forming what is known as Qena Fold, which distinguishes the governorate’s geographical features. This geological shape, in the opinion of many petroleum scientists, has helped form the quantities of crude oil found there.