Atlee received his early education in Lancaster except that in the winter of 1813-14 he attended the Gray and Wylie Academy of Philadelphia, a noted school of its day.
He intended to enter college; but his plans were upset by the death of his father, who left his widowed mother with six children, of whom John was the eldest.
At the age of eighteen, Atlee entered the medical department of the University of Pennsylvania, but, being too young for graduation the following year, he continued his studies with Dr. Humes, under whose direction in the winter of 1818-19 he attended many cases of variola, this being the first time the disease had made its appearance in America after the discovery of vaccination.
He attended another course of lectures at the University of Pennsylvania in the winter of 1819-20 and in the spring of 1820 received the degree of Doctor of Medicine.
After graduating from the University of Pennsylvania, he immediately began his medical career in his native town.
Although a general practitioner of medicine, Atlee's reputation was gained chiefly in surgery and obstetrics.
Cholera made its appearance in Lancaster in 1855. Atlee was an active member of the Sanitary Commission of Lancaster County which was formed to combat it. The deaths were but twenty-six (considered a small number at the time), due largely to the precautions taken by the Commission.
Medical organizations greatly interested Atlee from the beginning of his career. He was one of the founders of the Lancaster County Medical Society in 1844, was present at the birth of the State Medical Society in 1848, and in 1882 was made president of the American Medical Association.
He practised in his native town without interruption until the day of his death in 1885.
Atlee was for forty years a vestryman of St. James's Church of which he was a regular attendant.
Member of The Sanitary Commission of Lancaster County, member of the State Medical Society, member of the American Medical Association.
Atlee was a man of singular probity of character, with dignified bearing, which at once commanded attention and respect.
On March 12, 1822 he married Sarah Howell Franklin, daughter of Judge Walter Franklin of Lancaster County.