After practicing in Charleston, West Virginia, he moved to Decatur in 1915, becoming the first Black doctor in Macon County.  He was one of the forty-eight doctors to start the Decatur and Macon County Hospital in 1916, and practiced medicine until retiring in 1946.  In addition to his general practice, he was very influential in reducing tuberculosis among Black citizens in Decatur.

During his time in Decatur he also was active in Decatur Lodge No. 17 of the Prince Hall Freemasonry, the oldest active fraternal organization in the State of Illinois, and served as Grand Master for many years. In 1966 the chapter voted to change its name to the John C. Ellis Lodge No. 17.  In addition to his Masonic activities, Dr. Ellis served on the County Board of Supervisors; worked with the local NAACP chapter; and with his wife Henrietta was active at Antioch Missionary Baptist Church.  They moved to California in 1956 where he passed at the age of seventy-eight.  The “John C. Ellis Masonic Lodge” is located at 234 E Marietta Street, and in June 2025 the corner of East Marietta Street and North Water Street was named the Dr. John C. Ellis Parkway.