Ganji has been a human rights protagonist since his student days in the US, in the 1950s. The subject of his master's degree thesis was the United Nations and human rights, and his PhD dissertation was entitled "International Protection of Human Rights". Between 1961 and 1962 he served on the secretariat of the International Labour Organization and the division on the Application of the ILO Conventions and Recommendations. He later,1962–65, worked for the UN Division of Human Rights at the UN Headquarters in New York.
At the time of Shah Mohammad Reza Pahlavi's reign, Ganji convinced the Shah to invite the International Committee of Red Cross to open up permanent offices in Iran, to visit and inspect Iranian prisons and guarantee that no torture was taking place there. The ICRC offices remained open and active until after the Iranian Revolution, when the ruling clerics closed them down in 1980. Since the Iranian Revolution, Ganji has been active in bringing violations of human rights in Iran by the ruling clerics to the world's attention.
To save his life, Ganji hid in Iran and six months after the 1979 revolution escaped Iran on foot into Turkey and from there to the United States. Ganji is the founder and secretary general of the 'Derafsh Kaviani', a democratic non-violent opposition movement to the clerical regime. He is also founder and secretary general of the Organization for Human Rights and Fundamental Freedoms for Iran whose aims and purposes are educating the Iranian people about their rights and freedoms, demanding their respect by the authorities, and through civil disobedience striving towards the establishment of a free and pluralistic society respectful of human rights, the rule of non-discrimination, separation of church and state and a parliamentary democracy in Iran. Through the Flag of Freedom Organization of Iran and the Organization for Human Rights and Fundamental Freedoms for Iran, Ganji has been a leading advocate for freedom and human rights in Iran and has orchestrated a campaign of political defiance by advocating civil disobedience against the clerical regime in Iran since the revolution. During the past 30 years, seven attempts have been made against Ganji's life. Seven of his closest colleagues were assassinated in Europe and in the Middle East by the agents of the clerical regime. Many others are said to have been imprisoned, tortured and killed in Iran. Ganji is the author of many books and articles in Persian, English, and French. In addition to his 5 volumes of the United Nations Reports; these include university textbooks on international law and international organizations, international protection of human rights, apartheid and racial discrimination in southern Africa, Etre Persan, a study of the developments of the past fifty years in Iran written in Persian, entitled Atash-e Nahofteh, and Defying the Iranian Revolution: From a Minister to the Shah to a Leader of Resistance.