Daniel John Cunningham was born at Crieff on April 15, 1850. He was a son of the manse, and his father, the Rev. John Cunningham, subsequently became Principal of St Mary's College, St Andrews University. His mother was descended from a brother of Captain Porteous, of the Porteous Riot fame.

Daniel Cunningham was first educated at a small private school started by the heads of six families, who engaged a teacher for their boys. Ere long, however, Crieff Academy was organised, and to it the younger scholars were transferred. Cunningham received the simple, strong education of which Scotland was proud in those days, an education which fitted a promising boy for any walk in life. His first intention was to enter on a business career, and with this object in view he spent a year or two in Glasgow.