Baruch Kimmerling was born in Turda, Romania, and had cerebral palsy, a developmental disability. The family narrowly avoided the Holocaust by escaping from their village in a gypsy wagon. The family immigrated to Israel in 1952, and took up residence in a ma'abara (immigrants' camp), Sha'ar Ha'aliya, before moving to a small apartment on the outskirts of Netanya.

Despite his significant disabilities, which caused Kimmerling to experience motor difficulties and speech problems, his parents raised him as a typical child and encouraged him to strive high. He graduated from the Hebrew University in 1963, and obtained his PhD in 1973 as a sociologist. He made a name for himself in the academic world as a social historian, particularly for his groundbreaking work analyzing Jewish settlements in terms of colonialism. He was awarded a chair at the University of Toronto. He lectured widely and was a prolific writer of books and articles, extending his efforts beyond scholarly publications to numerous op-ed pieces in venues such as Haaretz and The Nation.

Kimmerling was an outspoken critic of Israeli policies, and spoke out on issues related to the Arab-Israeli conflict. He was dubbed one of Israel's "new historians," but insisted that he was a patriotic Zionist, dedicated to celebrating the diversities of cultures within Israel, and to the ideals of a secular state. Unlike some Israeli leftists, he publicly opposed the proposed boycott of Israeli academics by the Association of University Teachers in the United Kingdom, arguing that it would "weaken the last public sphere of free thinking and free speech in Israel."

Kimmerling died at the age of 67 after a long battle with cancer. He was buried in the secular cemetery at Kibbutz Mishmarot, leaving his wife, Diana Aidan, and three children.