The son of Mir Janaan Shah, he was born on 14th November 1963 in Kandahar, Afganistan. His father was a well known religious scholar in pre-war Afganistan. His initial education was conducted at home by his maternal grandfather, Sultan Shah, who was also a respected religious scholar and he later graduated from one of the best religious schools (madrasah) in Kabul. As a teenager, he joined a movement that was funded by Saudi Arabia to demolish Communism in Afghanistan. During the Soviet occupation of Afghanistan his family fled to neighbouring Pakistan, where he continued his studies in local madrassahs. He graduated from the madrassah of Moulana Sami-ul-haq (current Senator of M.M.A in Pakistan), and later joined the resistance forces in Afghanistan. He was well known among Afghan Mujahideen (freedom fighters ) and became an Amir (commander) of Panch So Kaman (500 soldiers) who were prominent in Tora Bora. In 1989, when the Soviet Union disintegrated and the Soviet Army left Afghanistan, Mir Alam joined the Engineer Hikmat Yaar Khan, a Saudi supported Mujahidden faction. Later, when American support ceased in Afghanistan, the mujahidden factions began fighting amongst themselves, Mir quit Engineer Hikmat Yaar and joined the Talba e Islam (students of Islam), later known as "Taliban". He was in the majlis - shoora Committe (the Islamic parliament) of Afghanistan. After 2001, when America invaded Afghanistan, Mir Shah fled back to Pakistan. He joined the Lal Qilla Madrassa of Peshawar. Mr. Shah was also affiliated with Al-Qaeda in Pakistan. He had a bounty on his head. On December 13th 2003, Mir Shah was shot dead in a police raid on his madrasah. He is buried in his family graveyard in Kandhar.
As of December 2006, the Pakistani government is cracking down on some religious schools, apparently because of their association with Mir Alam Shah and others like him.