Abdel Fattah al-Burhan was born in 1960 in the village of Qandto in River Nile State, north of the Sudanese capital Khartoum. He has seven brothers and two sisters, and he also has half-brothers and sisters from his father's second wife.

He married Fatima Suleiman, has three children (two sons and a girl), and lived the last years before the 3 revolution, moving between Yemen and the UAE. He fought military battles with the army during the southern war before the secession of South Sudan in 2011.