Kitamori was born in Kumamoto in 1916. In high school, he was so impressed by a paper he read about Martin Luther that he made the decision in 1935 to go to Tokyo to attend the Lutheran Theological Seminary there. He graduated in 1938.
Kitamori's early life was marked by a significant event when he read an article about Martin Luther in high school, inspiring him to pursue theological studies. This led him to make the decision in 1935 to travel to Tokyo to attend the Lutheran Theological Seminary, where he graduated four years later.