Among his many honors, Professor Humphrey was made an Officer of the Order of Canada in 1974, “in recognition of his contributions to legal scholarship and his world-wide reputation in the field of human rights”.
The John Peters Humphrey Model United Nations is held in his honour every May in Fredericton, New Brunswick.
Since 1988, the McGill University Faculty of Law has held the John P. Humphrey Lectureship in Human Rights, an annual lecture on the role of international law and organizations in the worldwide protection of human rights. 
The John Humphrey Freedom Award, presented by the Canadian human rights group Rights & Democracy, is awarded each year to organizations and individuals around the world for exceptional achievement in the promotion of human rights and democratic development. 
In June 2008, a memorial to Dr. Humphrey was unveiled in his hometown of Hampton, New Brunswick. The memorial, located just a few hundred yards from his childhood home, wooden bench in the form of the UN building with a young and old Humphrey seated. Several brass doves sit on the end of the bench, which sits beside two tall stone plinths, one of which has several articles from the Universal Declaration of Human Rights carved into it in English, French, Mi’kmaq and Maliseet-Passamaquoddy. The memorial sits on the front lawn of the County Court House in the center of the town.