The son of J. Sterling Morton, secretary of agriculture in Grover Cleveland's second administration, and cousin of Levi P. Morton, vice president during the presidency of Benjamin Harrison, Paul Morton was born in Detroit, Michigan, on May 22, 1857. He was raised in Nebraska, attending schools in Nebraska City, an establishment his parents founded. Morton would move to Chicago, Illinois, after turning eighteen. He worked for the Chicago, Burlington and Quincy Railroad, attaining the post of general freight agent. Morton would eventually rise to become president of the Atchison, Topeka, and Santa Fe Railroad. He became a "Gold Democrat" before switching to the Republican Party at the turn of the century. Both Morton's networking within the party and his merits in business led his appointment as secretary of the Navy by President Roosevelt. Morton assumed the post in June 1904, replacing outgoing secretary William H. Moody. Though he knew next to nothing about naval affairs, Morton was confirmed as secretary of the Navy on December 7, 1904.

A scandal ensued in February 1905 when the Interstate Commerce Commission asked the Justice Department to investigate charges that Morton acted illegally while head of the Colorado Fuel & Iron Company, charges that never resulted in prosecution but which forced Morton to resign quietly on July 1, 1905. Morton saved face by becoming vice chairman of the Moody Commission to reorganize the Navy in 1909. Paul Morton died unexpectedly on January 19, 1911, at the age of 53.