Boudiaf was killed by one of his own bodyguards, Lambarek Boumaarafi, presented officially as an Islamic fundamentalist, and a sympathiser of the Islamic Salvation Front (FIS), who acted alone. He was assassinated in Annaba while addressing a public meeting on June 29, 1992, which was later broadcast by the national TV.
He received 3 bullets, two in the head and one in his back. He was president for only five months, after his return from exile in Morocco to rule over the HCE (High Council of State) that emerged as a constitutional alternative to the Islamic State declared by the FIS after winning 1991 first democratic elections in the country since its independence in 1962. His mission was to crush the FIS, stop the civil war and restore order.
Boudiaf was one of the few lasting Algerian war veterans still alive at the time. After Krim Belkacem, assassinated in Frankfurt 1970, and Mohamed Khider assassinated in Madrid in 1967, and Mohammed Seddik Benyahia the foreign minister assassinated on the Iran–Iraq border when working on a walk out from the First Gulf War.
A month before his assassination he ordered the arrest of General Mostafa Beloucif, charged in front of the Blida tribunal of misusing public funds. Khaled Nezzar was also dismissed from his post of Defence Minister for the same reasons. Boudiaf also ordered the arrest of a Tamanrasset businessman involved in drugs and weapons traffic across the Sahel and Sub-Saharan Africa, but the colonel charged with the investigation was assassinated just a week before Boudiaf.