Dougherty, nicknamed "Dinny" by his parents, attended public school in Ashland until age 10, when he transferred to high school in Girardville. He worked as a breaker boy in the local coal mines during his summer vacations. After graduating from high school in 1880, he passed the entrance examinations for St. Charles Borromeo Seminary in Overbrook. However, at age 14, he was considered too young for admission, and was instead sent to Collège Sainte-Marie in Montreal, Quebec, Canada. After studying there for two years, he returned to Pennsylvania and finally entered St. Charles Seminary, where he skipped the first two years of training.