John was the son of William Wilson Compton and Nancy Carter Compton (William's first cousin). He married Mary E. "Mollie" Gregory and Margaret (Marguerite) Josephine Thorn. John and Mollie were the parents of George Moses Compton, Thomas Jefferson Compton, and Julia Belle Compton Ashworth. John and Margaret were the parents of William Thorn Compton and Wiley Buchanan Compton.

Notes on John Allen Compton, written by daughter Julia Ashworth:
"According to Johnnie Compton (Watson Compton's son), my father John A. Compton came to Kansas in 1877 and bought two quarters of land, one a school land grant and the other a railroad quarter grant. That was a few months before Uncle Watson came to Kansas. He returned to Virginia before Christmas 1878 and was married to Mary B. Gregory January 23, 1879. Coming back to Kansas, they lived on this land located southeast of Albert until sometime in 1883, when my mother, being so homesick, they sold the land and other possessions and returned to Virginia to make their home. However, after a few months there, they decided again to come back to Kansas which they did in October 1886. This explains how I [Julia] am the one of the children who was born in Virginia April 1885. They rented a place ten miles west of Gt. Bend and one mile north, but a few weeks later bought a quarter of land 5 1/2 miles north of Pawnee Rock where they planned to build a home. However in March 1887, my mother died after the birth of a daughter,of what they then called childbed fever. The baby died also a day or so later. My father then took me back to Virginia a few months later but kept George and Jeff. George was 8 and Jeff 5 at the time of their mother's death. In December 1891, he with the boys came to Virginia on a visit, and in March 1892, he was married to Josephine Thorn. A few days later the family returned to the home north of Pawnee where they lived until 1901 when my father had sold the home and moved to Pawnee County where we lived on what was then called the Gaheart farm until he completed buildings on land previously bought south of Ray and moved there Aug. 1903 where he lived until his death in May 1921. Two sons, Thorn and Wiley, who were born to him and his second wife, still live on the land there. Their mother died November 1932."