McCutcheon was born near South Raub, Tippecanoe County, Indiana to Captain John Barr McCutcheon and Clara Glick McCutcheon. He graduated from Purdue University, where he became a member of the Sigma Chi fraternity, in 1889 with a Bachelor of Science degree. At Purdue, he worked with typographer Bruce Rogers on the student newspaper and yearbook. There is now a dormitory at Purdue university and McCutcheon High School, in Tippecanoe County, Indiana, named in his honor.
He worked at the Chicago Morning News (later called the Chicago Record) and then at the Chicago Tribune from 1903 until his retirement in 1946.
He was the younger brother of novelist George Barr McCutcheon, writer of the "Graustark" books.
On the Purdue Campus, McCutcheon is memorialized in a coeducational dormitory, John T. McCutcheon Hall. The lobby displays an original of one of his drawings, a nearly life-size drawing of a young man.