At the outbreak of the French Revolution in 1789, Carnot entered political life. He became a delegate to the Legislation in 1791. While a member of the Legislative Assembly, Carnot was elected to the Committee for Public Instruction. Carnot believed all citizens should be educated and as a member of that committee, he wrote a series of reforms for the teaching and educational systems, but they were not implemented due to the violent social and economic climate of the Revolution. When the Legislative Assembly dissolved, Carnot was then elected to the National Convention in 1792. He spent the last few months of 1792 on a mission to Bayonne, organizing the military defense effort in an attempt to ward off any possible attacks from Spain. Upon returning to Paris, Carnot voted for the death of King Louis XVI, although he had been absent for the debates surrounding the king’s trial. On 14 August 1793 he was elected to the Committee of Public Safety where he took charge of the military situation as one of the Ministers of War.

The creation of the French Revolutionary Army was largely due to his powers of organization and enforcing discipline. In order to raise more troops for the war Carnot introduced conscription: the levée en masse approved by the National Convention was able to raise France’s army from a meager 645,000 troops in mid-1793 to 1,500,000 in September 1794. Once the problem of troop numbers had been solved Carnot turned his administrative skills to the supplies that this massive army would need. Many of the munitions and supplies were in short supply: copper was lacking for guns so he ordered church bells seized in order to melt them down; saltpeter was lacking and he called chemistry to his aid; leather for boots was scarce so he demanded and secured new methods for tanning. He quickly organized the army and helped to turn the tide of the war. It added significantly to discontent with the course of the Revolution in still Bourbon-loyalist areas — such as the Vendée, which had broken out in open revolt 5 months earlier — but the government of the time considered it a success, and Carnot became known as the Organizer of Victory. In autumn 1793, he took charge of French columns on the Northern Front, and contributed to Jean-Baptiste Jourdan's victory in the Battle of Wattignies.

He had taken no steps to oppose the Reign of Terror, but he, along with other technocrats on the committee like Robert Lindet and Louis-Bernard Guyton de Morveau, turned on Maximilien Robespierre and his allies during the Thermidorian Reaction.

With the establishment of the Directory in 1795, Carnot became one of the five initial directors. For the first year the Directors did well working harmoniously together as well as with the Councils. However, difference of political views led to a schism between Carnot and Étienne-François Letourneur. Later François de Barthélemy and the triumvirate of Paul François Jean Nicolas, vicomte de Barras, Jean-François Rewbell, and Louis Marie de La Révellière-Lépeaux. Carnot and Barthélemy both supported concessions to end the war, and hoped to oust the triumvirate and replace them with more conservative men. His and Étienne-François Letourneur's moderation was viewed as weakness, and it probably contributed to France's failure to capitalize on the Treaty of Campo Formio. After Letourneur had been replaced by another close collaborator of Carnot, François de Barthélemy, both of them, alongside many deputies in the Council of Five Hundred, were ousted in the Fructidor coup d'état of (4 September 1797), engineered by Generals Napoleon Bonaparte (originally, Carnot's protégé) and Pierre François Charles Augereau. He took refuge in Geneva, and there in 1797 issued his La métaphysique du calcul infinitésimal.

In 1800 he was appointed Minister of War by Bonaparte, and served in that office at the time of the Battle of Marengo. In 1802, he voted against the establishment of Napoleon's Consular powers for life and the passing of the title to his children, for as Carnot said when speaking of the power necessary to govern a state “If this power is the appendage of a hereditary family it becomes despotic.” After Napoleon crowned himself emperor on December 2, 1804, Carnot's republican convictions precluded his acceptance of high office under the First French Empire, and he resigned from public life — although he was later made a Count of the Empire by Napoleon as Lazare Nicolas Marguerite, comte Carnot.

In 1803 he produced his Géométrie de position. This work deals with projective rather than descriptive geometry, it also contains an elaborate discussion of the geometrical meaning of negative roots of an algebraic equation. Carnot returned to office in defense of Napoleon during the disastrous invasion of Russia; he was assigned the defence of Antwerp against the Sixth Coalition — he only surrendered on the demand of the Count of Artois, who was the younger brother of Louis XVIII and later Charles X.

During the Hundred Days, he served as Minister of the Interior for Napoleon, and was exiled as a regicide during the White Terror after the Second Restoration during the reign of Louis XVIII. He lived in Warsaw, and moved to Prussia, where he died in the city of Magdeburg. Carnot's remains were interred at the Panthéon in 1889, at the same time as those of Marie Victor de La Tour-Maubourg, Jean-Baptiste Baudin, and François Séverin Marceau-Desgraviers.

Carnot was able to survive and maintain a place of power during all the phases of the French Revolution, from its beginnings in 1789 until the fall of Napoleon in 1815. On the social and political front, Carnot was the author of many reforms that he thought to be for the good of the Republic. One of these was the proposal for compulsory public education for all citizens. He also penned a proposal for the new Constitution which included the “Declaration of the Duties of the Citizens” that held that there should be not only education but military service for all citizens of France between the ages of twenty and twenty-five. These proposals were in accordance with the Revolutionaries' thinking at the time, which held that men and women should be honored through ability and intelligence rather than through birthright, even though Carnot himself was nobly born. This style of thinking may well have been instrumental in Napoleon Bonaparte's rise to power as it was Carnot who promoted him from Captain to General.

But perhaps his greatest achievements, in deference to the French Revolution itself, were those of a military nature. If not for Carnot, the modern waging of war with mass armies and strategic planning would not exist. As a military engineer, Carnot favored fortresses and defensive strategies, but with the constant invasions decided to take his strategic planning to an offensive strike. From his intellect sprang the maneuvers and organization that turned the tides of war from 1793 to 1794. The basic idea was to have a massive army separated into several units that could move more quickly than the enemy and attack from the flanks rather than head on, which had led to resounding defeats before Carnot was elected to the Committee of Public Safety. This tactic was extremely successful against the more traditional tactics of existing European armies. It was his initiative to train the conscripts in the art of war and to place new recruits with experienced soldiers rather than having a massive volunteer army without any real idea of how to wage battle. He also created a new political strategy based on disrupting communication between enemy nations of England and Austria while concentrating attack effort on England. Carnot’s military influence and authority were eventually used to bring about the downfall of Robespierre.