 He was the grandson of famed surgeon John Collins Warren, Sr. and the Secretary of the Navy, Benjamin Williams Crowninshield, and also the great-grandson of surgeon John Warren.He was educated at Boston Latin School and at a private school run by Epes Sargent Dixwell, that was also attended by future Supreme Court Justice Oliver Wendell Holmes, Jr..He graduated from Harvard College (1863) and from Harvard Medical School (1866).