The appointment of William Schabas last year to head the commission had drawn strong criticism from Israel and the Harper government.
A spokesman for the UN Human Rights Council says Schabas submitted his resignation on Monday night.
The move followed an official Jan. 30 complaint from Israel accusing Schabas of "clear and documented bias against Israel, citing a "contractual relationship with the Palestinian side" prior to becoming head of the commission.
In his resignation letter, Schabas acknowledged that he received $1,300 for a legal opinion he wrote for the Palestine Liberation Organization in 2012.
However, Schabas said it was of a "technical legal nature" drawn from scholarly work he had published.
He also defended his record, saying that as a scholar involved in international human rights, he had "regularly condemned perpetrators of violations."
"This work in defence of human rights appears to have made me a huge target for malicious attacks," Schabas wrote, adding that he was resigning to avoid any distractions while the commission finished its "decisive stage" of work.
The UN commission was due to issue its report next month. Israel did not co-operate with it, saying it was hostile to Israel and that its conclusions were known in advance.
The 63-year-old Order of Canada officer, renowned for his work on international criminal and human rights law, was working as an international law professor at Middlesex University in England prior to joining the UN commission.
Hours after his appointment was announced in August 2014, then-foreign minister John Baird expressed his disdain on Twitter.
"It's an utter shame, and will do nothing to promote peace and dignity in Gaza for the Palestinian people," Baird wrote at the time.
Schabas once suggested in a speech that he believes Israeli Prime Minister Benjamin Netanyahu should be "in the dock of an international court.'' He also wrote in a law journal article that the Israeli prime minister could be regarded as "the single individual most likely to threaten the survival of Israel.''
Schabas said at the time of his appointment that the "suggestion that I'm anti-Israel is absurd."
Netanyahu has accused the UN commission of unfairly targeting Israel and ignoring abuses elsewhere.
"This is the same council that in 2014 made more decisions against Israel than against Iran, Syria and North Korea combined," Netanyahu said, adding that Gaza's Hamas rulers "need to be investigated, not Israel."
Hamas spokesman Fawzi Barhoum said Schabas' resignation "shows the huge pressure Israel and the Zionist lobby put on the committee and its chairman."
The Israeli pressure "is meant for impunity and killing the truth," Barhoum said.
The war in Gaza last summer killed more than 2,200 Palestinians and 72 people on the Israeli side. At least 1,483 Palestinian civilians were killed in the war — 66 per cent of the overall death toll — according to preliminary United Nations figures.
— With files from The Canadian Press.
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