Freeman was born in West Bridgton, Maine on his father's farm. He attended the country school in his hometown and public schools in Portland, Maine and Lawrence, Massachusetts. He entered the Massachusetts Institute of Technology in 1872, graduating with his BSc in civil engineering in 1876. After graduating, Freeman started his career at the Essex water power company as assistant to the company's engineer, Hiram F. Mills. In those days he became acquainted with other leading engineers such as Charles Storer Storrow, James B. Francis, Joseph R. Davis and John C. Hoadley. In 1886, he moved to Boston, where he was appointed engineer and inspector at the Associated Mutual Fire Insurance Company. In the next decades Freeman was the design engineer for several water projects, served on several water works commissions, and was consulting engineer for many projects. Freeman served as president of the American Society of Civil Engineers and of the American Society of Mechanical Engineers. He was also the founder and president of Massachusetts Mutual Fire Insurance Company. He was a member of the National Advisory Committee for Aeronautics during World War I, and served as chairman from 1918–1919. Freeman received numerous honorary degrees. He received Doctor of Science degrees from Brown University in 1904; from Tufts College in 1905; from the Sachsischen Technischen Hochschule in Dresden, Germany, in June 1925; from the University of Pennsylvania in 1927; and from Yale University in 1931. in 1922 he was awarded the ASME Medal. Freeman was elected Honorary Member of Phi Beta Kappa at Brown University in 1901; Member of the National Academy of Sciences in 1918; Honorary Member of the Marsaryk Academy of Works in Czechoslovakia in 1926; Ehrenbürger der Badischen Technischen Hochschule in Karlsruhe, Germany, in January 1929; Mitglied des Wissenschaftlichen Beirats des Forschungs-Institutes in München und Walchcnsee, Bavaria, Germany in January 1931; and Fellow of the American Academy of Arts and Sciences.
John Freeman, Regulation of elevation and discharge of the great lakes, 1926
John Freeman, Earthquake damage and earthquake insurance, 1932
John Freeman, Experiments relating to hydraulics of fire streams The nozzle as an accurate water meter.
John Freeman, Fire-stream tables.
John Freeman, Flow of water in pipes.
John Freeman, Hydraulic laboratory practice : comprising a translation, revised to 1929, of Die Wasserbaulaboratorien Europas, published in 1926 by Verein Deutscher Ingenieure; including also descriptions of other European and American laboratories and notes on the theory of experiments with models
John Freeman, Lock canal at Panama...
John Freeman, On contemporary technical education; address of John R. Freeman on behalf of the engineering societies at the inauguration of President Charles S. Howe, Case School of Applied Science.
John Freeman, On the safeguarding of life in theaters; being a study from the standpoint of an engineer.