Throughout the 1980s, relations with Chad, Sudan's neighbor on the west, were affected both by the civil strife in that country, which often spilled over into Darfur, and relations with Libya, which intervened in Chad's internal conflicts. At the time of the Bashir coup in June 1989, western Darfur was being used as a battleground by troops loyal to the Chadian government of Hissein Habré and rebels organized by Idris Deby and supported by Libya. Deby was from the Zaghawa ethnic group that lived on both sides of the Chad-Sudan border, and the Zaghawa of Darfur provided him support and sanctuary. Hundreds of Zaghawa from Chad had also fled into Sudan to seek refuge from the fighting. The RCC-NS was not prepared for a confrontation with Chad, which was already providing assistance to the SPLM, and thus tended to turn a blind eye when Chadian forces crossed into Darfur in pursuit of the rebels.

In May 1990, Chadian soldiers invaded the provincial capital of Al Fashir, where they rescued wounded comrades being held at a local hospital. During the summer, Chadian forces burned eighteen Sudanese villages and abducted 100 civilians. Deby's Patriotic Movement for Salvation (Mouvement Patriotique du Salut) provided arms to Sudanese Zaghawa and Arab militias, ostensibly so that they could protect themselves from Chadian forces. The militias, however, used the weapons against their own rivals, principally the ethnic Fur, and several hundred civilians were killed in civil strife during 1990. The government was relieved when Deby finally defeated Habré in December 1990. The new government in N'Djamena signaled its willingness for good relations with Sudan by closing down the SPLM office. Early in 1991, Bashir visited Chad for official talks with Deby on bilateral ties.

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Source: U.S. Library of Congress