On returning to France he received the appointment of inspector of public buildings at Belfort, where be studied fortification and military science. In 1792 he enlisted in the Haut-Rhin volunteers. Due to his military knowledge he at once gained election as adjutant and soon afterwards as lieutenant-colonel.
At the defence of Mainz (July 1793) he so distinguished himself that though disgraced along with the rest of the garrison and imprisoned, he promptly won reinstatement, and became in August 1793 general of brigade. He won considerable distinction in the Vendéan war, and two months later gained promotion to general of division. In these operations began his intimacy with Marceau, with whom he defeated the Royalists at Le Mans and Savenay. When he openly expressed his opinion that the Vendéans merited lenient measures, the authorities recalled him; but re-instated him once more in April 1794 and sent him to the Army of the Sambre-and-Meuse.
He displayed his skill and bravery in the numerous actions around Charleroi, and especially in the crowning victory of Fleurus (26 June 1794), after which in the winter of 1794 - 1795 he besieged Mainz. In 1795 and again in 1796 he held the chief command of an army temporarily, but declined a permanent appointment as commander-in-chief. On 13 October, 1795 he fought a brilliant rearguard action at the bridge of Neuwied, and in the offensive campaign of 1796 he served as Jourdan's most active and successful lieutenant.
Having, after the retreat to the Rhine, declined the chief command, he withdrew into private life early in 1798. He accepted a division in the expedition to Egypt under Bonaparte, but suffered a wound in the head at Alexandria in the first engagement, which prevented his taking any further part in the campaign of the Pyramids, and caused his appointment as governor of Alexandria. In the Syrian campaign of 1799, however, he commanded the vanguard, took El-Arish, Gaza and Jaffa, and won the great victory of Mount Tabor on 15/16 April 1799.
When Napoleon returned to France towards the end of 1799 he left Kléber in command of the French forces. In this capacity, seeing no hope of bringing his army back to France or of consolidating his conquests, he negotiated the convention of El-Arish (24 January 1800) with Admiral Smith, winning the right to an honorable evacuation of the French army. But when Admiral Lord Keith refused to ratify the terms, Kléber attacked the Turks at Heliopolis, though he had only 10,000 men against 60,000, and utterly defeated them on 20 March 1800. He then re-took Cairo, which had revolted from the French.
Shortly after these victories, a Syrian student, Soleyman El-Halaby, living in Egypt, assassinated Kléber by knifing him through the heart at Cairo on 14 June, 1800, the same day on which his friend and comrade Desaix fell at Marengo. His assassin was executed by Impalement in a public square in Cairo after his right arm was burned off, and left for several hours to die. His skull was shipped to France and used to teach French medical students what the French authorities claimed was the bump of "crime" and "fanaticism"
"Kléber emerged as undoubtedly one of the greatest generals of the French revolutionary epoch. Though he distrusted his powers and declined the responsibility of supreme command, there is nothing in his career to show that he would have been unequal to it. As a second-in-command no general of his time excelled him. His conduct of affairs in Egypt at a time when the treasury was empty and the troops were discontented for want of pay, shows that his powers as an administrator were little - if at all - inferior to those he possessed as a general."