Habré was born in 1942 in Faya-Largeau, northern Chad, then a colony of France, into a family of shepherds. He is a member of the Anakaza branch of the Daza Gourane ethnic group, which is itself a branch of the Toubou ethnic group. After primary schooling, he obtained a post in the French colonial administration, where he impressed his superiors and gained a scholarship to study in France at the Institute of Overseas Higher Studies in Paris. He completed a university degree in political science in Paris, and returned to Chad in 1971. He also obtained several other degrees and earned his Doctorate from the Institute. After a further brief period of government service as a deputy prefect, he visited Tripoli and joined the National Liberation Front of Chad (FROLINAT) where he became a commander in the Second Liberation Army of FROLINAT along with Goukouni Oueddei. After Abba Siddick assumed the leadership of FROLINAT, the Second Liberation Army, first under Oueddei's command and then under Habré's, split from FROLINAT and became the Command Council of the Armed Forces of the North (CCFAN). In 1976 Oueddei and Habré quarreled and Habré split his newly named Armed Forces of the North (Forces Armées du Nord or FAN) from Goukouni's followers who adopted the name of People's Armed Forces (Forces Armées Populaires or FAP). Both FAP and FAN operated in the extreme north of Chad, drawing their fighters from the Toubou nomadic people.
Habré first came to international attention when a group under his command attacked the town of Bardaï in Tibesti, on 21 April 1974, and took three Europeans hostage, with the intention of ransoming them for money and arms. The captives were a German physician, Dr. Christoph Staewen (whose wife Elfriede was killed in the attack), and two French citizens, Françoise Claustre, an archeologist, and
Marc Combe, a development worker. Staewen was released on 11 June 1974 after significant payments by West German officials. Combe escaped in 1975, but despite the intervention of the French Government, Claustre (whose husband was a senior French government official) was not released until 1 February 1977. Habré split with Oueddei, partly over this hostage-taking incident (which became known as the "Claustre affair" in France).