Pétion was born in Port-au-Prince to a black mother and a French father. He was sent to France in 1788 to study at the Military Academy in Paris. He returned to take part in the expulsion of the British (1798-99). His mulatto heritage meant that when tensions arose between blacks and mulattoes he supported the mulatto faction. He allied with General André Rigaud and Jean Pierre Boyer against Toussaint L'Ouverture in the failed rebellion, the so-called War of Knives, which began in June 1799. By November the rebels were pushed back to the strategic southern port of Jacmel, the defence was commanded by Pétion. The town fell in March 1800 and the rebellion was effectively over. Pétion and other mulatto leaders went into exile in France.
He returned in February 1802 with Boyer, Rigaud and the 12,000 strong French army commanded by Charles Leclerc. Following the treacherous treatment of Toussaint and the renewed struggle he joined the nationalist force in October 1802 following a secret conference at Arcahale and supported Jean-Jacques Dessalines, the general who had captured Jacmel. The capital was taken on October 17, 1803 and independence was declared on January 1, 1804. Dessalines was made ruler for life and had himself crowned emperor on October 6, 1804.
Following the death of Dessalines in October 1806, Pétion championed democracy and clashed with Henri Christophe. Christophe was offered a democratic presidency, but this failed. The country divided between them and the tensons between the blacks and mulattoes were reignited. After the inconclusive struggle dragged on until 1810 a peace was agreed and the country was split in two. While Christophe made himself king, Pétion had himself elected President of the southern part of Haiti in 1806. Initially a supporter of democracy he found the constraints imposed on him by the senate onorous and suspended the legislature in 1818. In 1816 he turned his post into President for Life.
He was active in seizing the commercial plantations and divided the land thus gained amongst his supporters and the peasantry, earning himself the nickname Papa Bon-Kè ("good-hearted daddy"). The land grab dealt a serious blow to the economy of the country and most of the population did little more than subsistence farming. He started the Lycée Pétion in Port-au-Prince. He gave sanctuary to Simón Bolívar in 1815 and provided him with material support.