Khalil cofounded Harakat-ul-Jihad-ul-Islami (HuJI) in 1980 with Irshad Ahmad and Qari Saifullah Akhtar, all three had graduated from Jamia Uloom-ul-Islamia Banuri Town in Karachi. He would later go on to found and lead Harkat-ul-Mujahedeen.[2] Khalil was a signatory of Osama bin Laden's 1998 fatwa called the International Front Against Jews and Crusaders.[2][3]