Born in Baltimore, Maryland, he was the son of Jerome Napoleon Bonaparte (1805-70) and Susan May Williams (1812-1881), from whom the American line of the Bonaparte family descended.
After graduating from Harvard University and Harvard Law School, where he would later be appointed a university overseer, he practiced law in Baltimore and became prominent in municipal and national reform movements.
On September 1, 1875, Charles Joseph Bonaparte married Ellen Channing Day (1852-1924). They had no children.
He was a member of the Board of Indian Commissioners from 1902 to 1904, chairman of the National Civil Service Reform League in 1904 and appointed a trustee of the Catholic University of America. In 1905, United States President Theodore Roosevelt appointed Bonaparte to his cabinet as United States Secretary of the Navy. From 1906 until the end of President Roosevelt's administration he served as United States Attorney General. He was active in suits brought against the trusts and was largely responsible for breaking up the tobacco monopoly. In 1908 Joseph founded the Federal Bureau of Investigation (FBI).
He was one of the founders, and for a time the president, of the National Municipal League.
Charles Joseph Bonaparte died in Bella Vista, Baltimore County, Maryland.