Ben-Ami was born in Tangiers, Tangier International Zone, on 17 July 1943, and immigrated to Israel in 1955. He was educated at Tel Aviv University and St Antony's College, Oxford from which he received a D.Phil. in history. Ben-Ami speaks fluent Hebrew, Spanish, French and English.
He was a historian at Tel Aviv University from the mid-1970s, serving as head of the School of History from 1982 to 1986. He later turned his attention to the history of Israel and the Middle East, leaving a legacy of expertise in Spanish inter-war year politics.
From 1987 until 1991, before he entered politics, he was the Israeli ambassador to Spain. In 1996 he was elected to the Knesset on Labour's list.
When the One Israel-led government of Ehud Barak took office in July 1999, Ben-Ami became the Minister of Internal Security, responsible for the Israel Police. In August 2000, when David Levy resigned as Foreign Ministerduring talks with Palestinian leaders in the United States, Barak designated Ben-Ami to be the acting Foreign Minister and he was officially appointed to the role in November 2000.
Ben-Ami remained Foreign Minister and Security Minister until March 2001, when, having won elections, Ariel Sharon took over from Barak. Ben-Ami refused to serve in the Sharon government and resigned from the Knesset in August 2002.
In their report published in 2003, the Or Commission held him responsible for the behavior of security forces during the October 2000 riots in which Israeli police killed 12 Israeli Arabs and one Palestinian, and failed to predict and control rioting which resulted in the death of a Jewish Israeli. The report recommended that Ben-Ami be disqualified from serving as Internal Security Minister in the future. Despite the disqualification, Ben-Ami was not considered to be a hard-liner in Israeli relations with the Palestinians and during his time in the Barak government, he was a political rival of Shimon Peres.
Ben-Ami is currently Vice-President of the Toledo International Centre for Peace (TICpax), which, according to its mission statement, "seeks to contribute to the prevention and resolution of violent or potentially violent international or intranational conflicts and to the consolidation of peace, within a framework of respect and promotion of Human Rights and democratic values."
His latest book is Scars of War, Wounds of Peace: The Israeli–Arab Tragedy (Oxford, 2006) challenges many of the founding myths in Israel's modern history especially related to the war of independence. Ben-Ami backed the Meretz party for the 2009 Knesset elections.
He currently serves as vice president of the Toledo International Centre for Peace of which he is a co-founder. Through the Center, he has been involved in conflict resolution processes such as among others, in Colombia, Dominican Republic ( the tensions with Haiti ), Bolivia ( intercultural issues ), Russia-Georgia, Libya ; Spanish Sahara, and Israel-the Arab world. He is now also the co-chair ( together with ex-chief of Mossad Efraim Halevi ) of an Israeli commission for strategic planning. He has lectured extensively in international conferences in Europe, Russia, the U.S. and Latin America.