Charles married Myrtle in Clinton, Missouri, on March 29, 1881, and the newlyweds moved to Pueblo, Colorado, where Charles established a real estate business with the brother-in-law of Nona Lovell Brooks, who was later to found the Church of Divine Science.
After the births of their first two sons, Lowell Page and Waldo Rickert Fillmore, the family moved to Kansas City, Missouri. Two years later, in 1886, Charles and Myrtle attended New Thought classes held by Dr. E. B. Weeks. Myrtle subsequently recovered from chronic tuberculosis and attributed her recovery to her use of prayer and other methods learned in Weeks' classes. Subsequently Charles began to heal from his childhood accident, a development that he, too, attributed to following this philosophy. Charles Fillmore became a devoted student of philosophy and religion.