John Harvey Kellogg was born in Tyrone, Michigan, to John Preston Kellogg and Ann Janette Stanley. Growing up in a large and devout Seventh-day Adventist family, his early life was heavily influenced by the religious beliefs and health reform principles that would later shape his career.

After attending medical school at the University of Michigan, Kellogg completed his training at Bellevue Hospital Medical College in New York City. This marked the official beginning of his medical career, equipping him with the formal knowledge he would later apply, and sometimes controversially adapt, at the Battle Creek Sanitarium.