Unable to enter the elite naval schools, he entered the navy as a volontaire in 1768. In 1773, he served as a lieutenant on the Atalante in the Indian Ocean. In 1778, he distinguished himself at the siege of Pondicherry, earning the rank of capitaine de brûlot (fireship captain).
He then served under Suffren, who gave him command of the frigate Bellone after the battle of Cuddalore. He was later transferred to the frigate La Dauphine, and became first officer aboard the Suffren's ship of the line Le Brillant.
In 1782, Suffren made him his aide, and gave him a seemingly impossible mission: Escape the English fleet and warn the two ships of the line and two frigates blockading Madras about a superior English fleet. "You will probably be taken on your way out or on your way back, make out as you can, but fight well!". He set out in the small frigate Naïade. After 4 days, he encountered the 64-gun HMS Spectre. Villaret eluded his opponent by sailing in shallow waters, where his larger and heavier opponent could not follow. Close to Madras, he finally engaged the English ship, striking his colours after a 5-hour battle, Naïade having over two metres of water in her hull. The English captain refused to accept Villaret's sword, saying: "Sir, you have given us a fairly beautiful frigate, but you made us pay dearly for her!". Villaret was taken prisoner, but the sound of the battle had warned the French squadron which escaped. Villaret was exchanged in 1783, and made Grand Cross of the Order of Saint Louis in July. He was promoted to lieutenant de vaisseau in 1784 for his service. After the war, Villaret served in the harbour of Lorient.Revolution.
In 1791, he was given command of the frigate Prudente to transport troops to Saint-Domingue. Arriving shortly before the slave revolt that launched the Haitian Revolution, he helped the governor transport troops around the island.
On 14 March 1792, he swore the "civic oath" to the Republic, while his brother emigrated. Promoted to Capitaine de Vaisseau in 1792, he was given the command of a ship-of-the-line, Trajan. In 1793, he commanded a small squadron patrolling the coast of the Vendée, in order to prohibit the British from aiding the Vendéan Revolt. When the rest of the Brest fleet sailed to Belle-Isle, a mutiny broke out among many ships in the fleet, Villaret was one of the few officers who maintained order aboard his ship.
In 1794, Jeanbon Saint André named Villaret-Joyeuse as the commander of the Brest Fleet because of his ability to maintain discipline aboard his ship during the turmoil of the revolution. The same year, Villaret was promoted to contre-amiral. Assisted by Saint André, Villaret reorganised and revitalised the Brest fleet. Among other measures, Saint André and Villaret-Joyeuse founded a naval artillery school.Battles of Prairial, of which the British referred to the main engagement as the Glorious First of June. Although defeated, he rallied his remaining ships and rescued five ships that had surrendered and the grain convoy reached Brest unmolested.
Supported by Saint-André, Villaret-Joyeuse kept his command despite the defeat. He blamed the defeat on the conduct of several of his captains who had failed to fulfil their duties. In September 1794, Villaret-Joyeuse was promoted to vice-amiral. In December, the Committee of Public Safety ordered him to attack British commerce in the Croisière du Grand Hiver. Although the cruise did lead to the capture of a number of British merchant ships, the French fleet was battered by storms in which several ships were sunk and all the surviving ships suffered heavy damage. In June 1795, he sailed with 9 ships to relieve a small squadron near Belle Île. During the First Battle of Ile de Groix, Villaret-Joyeuse chased away the small British squadron blockading Belle Île. Unable to bring them to battle, Villaret attempted to return to Brest, but contrary winds forced him towards Lorient. Close to Lorient, Villaret-Joyeuse was discovered by British admiral Alexander Hood's fleet, guarding the expedition to Quiberon. During Second Battle of Ile de Groix, several of Villaret's ships disobeyed his orders and sailed away, abandoning three ships to the British.
In 1796, Villaret-Joyeuse resigned in protest against the state of the Navy and in opposition to the Directory's plan to invade Ireland, instead of a campaign in the Indian Ocean.
He cooperated with Admirals Missiessy and Villneuve who sailed into the Caribbean in 1805. In January 1809, a British expedition invaded Martinique and laid siege to the fortress at Fort-de-France. The month-long siege ended on 24 February when the British were able to bring up their heavy artillery.
Upon his return to France, Napoleon, who was angered at the surrender, had Villaret court-martialed for surrendering the island too quickly. Initially found guilty, Villaret pleaded his case and eventually received a pardon from Napoleon in 1811: "Bravery and fidelity plead in favour of the vice-admiral (...) did his faults lose the colony? At most, they shortened its keeping for a few days." As Napoleon prepared for the invasion of Russia, he named Villaret governor of Venice in April 1811, where he was occupied with the maritime affairs. Villaret retained this position until 24 July 1812 when he died of edema.
To honour him, Napoleon had his name engraved on the Arc de Triomphe in Paris.