After the Egyptian campaign, Rapp remained under the command of Desaix until the latter's death at Marengo on 14 June 1800. He then became aide-de-camp of Napoleon, then the First Consul, a post he held until 1814. Under this title, he was charged with many confidential missions by Napoleon in the Vendée, Switzerland and Belgium. In 1803 he was promoted to brigadier general and in December 1805, he led a memorable attack at Austerlitz, when he charged at the head of two squadrons each of the Mounted Chasseurs and the Mounted Grenadiers of the Guard and the Guard Mameluks and decimated the Chevalier Guards of the Russian Imperial Guard. Promoted to division general, he later fought at Jena on 14 October 1806 and was wounded at Golymin.