The organization was formed in Iran in 1982 as the military wing of the Supreme Council for Islamic Revolution in Iraq. It was based in Iran for two decades during the rule of Saddam Hussein and led by Iranian officers. It consisted of several thousand Iraqi exiles, refugees, and defectors who fought alongside Iranian troops in the Iran–Iraq War. The group was armed and directed by Iran. They briefly returned to Iraq in 1991 during the 1991 Iraqi uprising to fight against Saddam Hussein, focusing on the Shia holy cities of Najaf and Karbala. They retreated back into Iran after the uprising was crushed. In 1995, during the Kurdish Civil War, Iran deployed 5,000 Badr fighters to Iraqi Kurdistan.
Returning to Iraq following the 2003 coalition invasion, the group changed its name from brigade to organization in response to the attempted voluntary disarming of Iraqi militias by the Coalition Provisional Authority. It is however widely believed the organization is still active as a militia within the security forces and it has been accused of running a secret prison and sectarian killings during the Iraqi Civil War. Because of their opposition to Saddam Hussein, the Badr Brigade was seen as a U.S. asset in the fight against Baathist partisans. After the fall of Baghdad, Badr forces reportedly joined the newly reconstituted army, police, and Interior Ministry in significant numbers. The Interior Ministry was controlled by SCIRI, and many Badr members became part of the Interior Ministry run Wolf Brigade. The Iraqi Interior Minister, Bayan Jabr, was a former leader of Badr Brigade militia. In 2006 the United Nations human rights chief in Iraq, John Pace, said that hundreds of Iraqis were being tortured to death or executed by the Interior Ministry under SCIRI's control. According to a 2006 report by the Independent newspaper: 'Mr Pace said the Ministry of the Interior was "acting as a rogue element within the government". It was controlled by the main Shia party, the Supreme Council for Islamic Revolution in Iraq ; the Interior Minister, Baqir Jabr al-Zubeidi, is a former leader of SCIRI's Badr Brigade militia, which was one of the main groups accused of carrying out sectarian killings. Another was the Mahdi Army of the young cleric Muqtada al-Sadr, who is now part of the Shia coalition seeking to form a government after winning the mid-December election. Many of the 110,000 policemen and police commandos under the ministry's control are suspected of being former members of the Badr Brigade. Not only counterinsurgency units such as the Wolf Brigade, the Scorpions, and the Tigers, but the commandos and even the highway patrol police were accused of acting as death squads during this period over a decade ago. The paramilitary commandos, dressed in garish camouflage uniforms and driving around in pick-up trucks, were dreaded in Sunni neighbourhoods. People arrested by them during this period were frequently found dead several days later with their bodies bearing obvious marks of torture.'