John Pemberton married Ann Eliza Clifford Lewis. This union was a central part of his life and provided him with domestic stability.

John and Ann Pemberton welcomed their son, Charles Pemberton, into the world. Charles later played a role in the Coca-Cola story, selling portions of what he claimed was his father's formula after John's death.

While specific details are limited, it is evident that Pemberton maintained relationships with his extended family. His father, James Clifford Pemberton, and mother, Martha Patsy Gay Pemberton, influenced his early life, and he likely maintained contact with them and other relatives throughout his adult years.

Following his war wound, Pemberton's dependence on morphine heavily impacted his personal life. It likely strained his relationships and contributed to his financial and health struggles in his later years.