A grandson of Clarence Talmadge Brown, the first Protestant minister to gather a congregation in Salt Lake City, Gilkey grew up in Hyde Park, Chicago.

His father Charles Whitney Gilkey was a liberal theologian and the first Dean of the University of Chicago's Rockefeller Chapel; his mother was Geraldine Gunsaulus Brown who was a well known feminist and leader of the YWCA.

In 1940, he earned a Bachelor of Arts in philosophy, magna cum laude, from Harvard University, where he lived in Grays Hall during his freshman year.

[3] After the war, Gilkey obtained his doctorate in religion from Columbia University in New York, being both mentored by and a teaching assistant to Reinhold Niebuhr.

[1] During this last period of his teaching career, he was also for three months a visiting professor at the Theology Division (now Divinity School) of Chung Chi College, the Chinese University of Hong Kong.

In the 1970s and 1980s, Gilkey's theological vision was colored by the growth of Buddhism, and Sikhism as both religions began to influence religious life in America.