John Kerr Pepper was born on October 19, 1837, in North Carolina to John Pepper. His father was a doctor who owned $12,000 of real estate and $10,000 of personal property by 1860. Pepper grew up and attended school in Stokes County, North Carolina, and by 1860, he was also working as a doctor.
On May 29, 1861, he received a commission as a 2nd lieutenant in Company F of the 21st North Carolina Infantry. The regiment took part in the First Battle of Bull Run. Pepper resigned on April 26, 1862. He soon returned to the Confederate army: by September 1863, he was serving as a sergeant in Company D of the 52nd North Carolina Infantry. The regiment took part in the Overland Campaign. He fell ill in May 1864, and he spent the next few months at home recovering. He remained in the army until at least November 1864.
Pepper returned to Stokes County after the war, and he married Judith E. Kerner. They had at least three children: Rufus, born around 1874; Nathaniel, born around 1877; and Mary, born around 1879. He worked as a dry goods merchant, and he died on March 27, 1885.