According to most sources, Omar was born sometime between 1950 and 1962 in a village in Kandahar Province, Kingdom of Afghanistan (in present-day Kandahar Province or Uruzgan Province). Some suggest his birth year as 1950 or 1953, or as late as around 1966. According to a "surprise biography" published by the Taliban in April 2015, he was born in 1960. His exact place of birth is also uncertain; one possibility is a village called Nodeh near the city of Kandahar.

On 29 July 2015, the Afghan government publicly announced that Mohammed Omar had died in 2013. Pakistani newspaper The Express Tribune reported that a former Afghan Taliban minister and current leadership council member, who spoke on condition of anonymity, said Mullah Omar died from tuberculosis. It was confirmed by a senior Taliban member that Omar's death was kept a secret for two years. It is alleged that Omar was "buried somewhere near the border on the Afghan side". The place of Omar's death is disputed; according to Afghan government sources, he died in a hospital in Karachi, Pakistan. A former Taliban minister stated that Karachi was "Omar's natural destination because he had lived there for quite some time and was as familiar with the city as any other resident." However, this claim has been dismissed by other Taliban members, stating that his death occurred in Afghanistan after his health condition had deteriorated due to "sickness" and that "not for a single day did he go to Pakistan". According to an official statement by Pakistani defence minister Khawaja Asif, "Mullah Omar neither died nor was buried in Pakistan and his sons' statements are on record to support this. Whether he died now or two years ago is another controversy which we do not wish to be a part of. He was neither in Karachi nor in Quetta." Initially, some Taliban members denied that he had died. Other sources considered the report to be speculative, designed to destabilise peace negotiations in Pakistan between the Afghan government and the Taliban. Abdul Hassib Seddiqi, the spokesman for Afghanistan's National Directorate of Security (NDS), said: "We confirm officially that he is dead."  The following day, the Taliban confirmed the death of Omar. Sources close to the Taliban leadership said his deputy, Mullah Akhtar Mansour, would replace him, although with the lesser title of Supreme Leader. Omar's eldest son, Mullah Mohammad Yaqoob, was opposed to Mansour's ascension as leader.  The Taliban splinter group Fidai Mahaz claimed Omar did not die of natural causes but was instead assassinated in a coup led by Mullah Akhtar Mansour and Mullah Gul Agha. The Taliban commander, Mullah Mansoor Dadullah, brother of former senior commander Mullah Dadullah, confirmed that Omar had been assassinated. The leader of Fidai Mahaz, Mullah Najibullah, revealed that due to Omar's kidney disease, he needed medicine. According to Najibullah, Mansour poisoned the medicine, damaging Omar's liver and causing him to grow weaker. When Omar summoned Mansour and other members of Omar's inner circle to hear his will, they discovered that Mansour was not to assume leadership of the Taliban. It was due to Mansour allegedly orchestrating "dishonourable deals." When Mansour pressed Omar to name him as his successor, Omar refused. Mansour then shot and killed Omar. Najibullah claimed Omar died at a southern Afghanistan hide-out in Zabul Province in the afternoon on 23 April 2013. Mullah Mohammad Yaqoob, Mullah Omar's elder son, denied that his father had been killed, insisting that he died of natural causes.  Omar's death brought about condolences from Ajnad al-Kavkaz, Ansar al Furqan, Islamic Front's Ahrar al-Sham, Jaish Muhammad, Jabhat Ansar al Din, Turkistan Islamic Party, Jamaat Ansar al Sunnah, Jaish al Ummah, Jamaat ul Ahrar, Caucasus Emirate, Jaish al-Islam, Nusra, AQAP, and AQIM, and Al-Shabaab.

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