With the rank of Captain, Perrée acted as a Chief of Division during the French expedition to Egypt: General Bonaparte appointed him to the Nile flotilla, where he commanded a squadron of shebeks and other light craft. On 13 July, the flotilla fought against Egyptian fluvial ships and forts while supplying food and ammunition to the French Army, and Perrée managed to captured some of these ships and ward off the others. Wounded during the prelude of the Battle of Shubra Khit, Perée was promoted to Rear-admiral on the insistence of Bonaparte, and received a sabre of honour inscribed ""Bataille de Chabreis"" on one side of the blade, and ""Donné par le général Bonaparte"" on the other.