Goukouni is from the northern half of the country and is the son of Oueddei Kichidemi, derde of the Teda. He entered politics in the late 1960s as a militant in the National Liberation Front of Chad led by Abba Siddick. FROLINAT resented the political dominance enjoyed by southerners under the presidency of François Tombalbaye and advocated the participation of central and northern peoples. After Tombalbaye's assassination in 1975, tensions between the two geographical halves escalated into a convoluted civil war that involved several Chadian political groups, Libya, the United States, and France. The conflict was to last through the 1980s. Goukouni viewed the dictatorial Tombalbaye regime as an instrument of continued French hegemony in Chad.
By 1983, Goukouni returned to Chad with substantial Libyan assistance to fight the Habré régime through guerrilla warfare. He was the most recognized Chadian oppositionist, whose views carried significant weight, though Habré granted only limited concessions in an attempt to reconcile with Goukouni. The former president reportedly demanded a new constitution and liberalization of political party activity, which Habré did not accede to. He was placed under house arrest in August 1985 in Tripoli when the Libyan government disapproved his intentions of negotiating a truce with Habré. In October 1985, Libyan police arrested Oueddei, and in the process they shot him in the stomach. He then broke with the Libyans and went into exile in Algiers instead in February 1987. However, some questioned whether he had truly broken with the Libyans, and in July 1987 Oueddei said that he was on good terms with them. Goukouni met with Chadian President Idriss Déby on April 17, 2007, in Libreville, Gabon, to discuss ways to end a civil war. Saying that Chad was in grave danger, Goukouni expressed a hope that he could use his "moral authority" to save it. He said that in turn he wanted to be allowed to return to Chad from exile in the future, and he said that Déby had agreed to that. On April 19, the leaders of two rebel groups rejected Goukouni's offer to mediate. Goukouni returned to Chad on July 30, 2007, along with about twenty other exiled opponents of the regime, for a discussion with Déby regarding the rebellion and how to resolve the situation. Goukouni and the others left Chad and returned to Libreville later on the same day. He met with Nigerien President Mamadou Tandja on March 4, 2008, discussing the situation in Chad following the February 2008 Battle of N'Djamena. In 2013 his youngest child, Saadie Goukouni Weddeye, was appointed to the Chadian government as Minister of Social Action.
Special envoy
Amidst the 2015 Burundian unrest, central African leaders, including Déby, designated Goukouni as special envoy to the Great Lakes region on 25 May 2015 in order to help resolve the situation in Burundi.