It was founded in 2004 as the Canadian Council for Israel and Jewish Advocacy (CCIJA) and headquartered in the district of North York within Toronto, Ontario.

[8] CIJA has faced criticism due to comments made by staff through news outlets and via its social media accounts.

In 2023, Canadians for Justice and Peace in the Middle East criticized "provocative statements" made by CIJA Israel office Director David M. Weinberg.

His statements make use of dehumanizing terms to refer to Arabs, Muslims, Palestinians, and human rights activists, calling them “weeds”, “snakes”, “barbarians”, and “terrorists”.

[9][10] CIJA also faced criticism when it lobbied against islamophobia Motion M103 in a Canadian parliamentary committee, just weeks after the Quebec City mosque shooting, together with B'nai B'rith Canada.