Birju Dattani announced his resignation in a LinkedIn post Monday, saying "I have agreed to resign as Chief Commissioner of the Canadian Human Rights Commission, effective today."
"I remain a steadfast believer in the Commission's work, mandate, and its importance to our democracy."
Canada's Human Rights Commission looks into human rights complaints against Canada's federal government, among other things.
Dattani was appointed in June, but his appointment was met with opposition from some Jewish groups.
Among other things he was accused of tweeting "Palestinians are Warsaw Ghetto Prisoners of Today"; and of participating in panels on Israel Apartheid Week and the Boycott, Divestment and Sanctions movement.
The investigation into him found that he did not harbour any beliefs that would be characterized as anti-Semitic, and that he did not demonstrate any biases towards Jews or Israelis.