Henrik Pontoppidan was born July 24, 1857, in Fredericia—located on the Jutland Peninsula of Denmark. . His father, Dines Pontoppidan, was a Lutheran clergyman, one in a long line of family ministers, and an advocate of fanatic spiritualist N. F. S. Grundtvig.
Pontoppidan's mother, Marie Kirstina (Oxenböll), was the daughter of a Danish government official.
The fourth of sixteen children, Pontoppidan was expected to carry on the theological tradition for the family, but surprised everyone and disappointed his father when he decided to pursue engineering instead.