He was the son of Elinor (née Fatman) and Henry Morgenthau Jr., who served as the Secretary of the Treasury under Presidents Franklin Delano Roosevelt and Harry Truman from 1934 until 1945.

Before going into diplomatic service, Henry Morgenthau Sr. had made a fortune in real estate, and became a strong financial backer of Democratic President Woodrow Wilson.

The family home was near Franklin Delano Roosevelt's Springwood Estate at Hyde Park, New York, and he grew up acquainted with the future President.

He took his 30-day midshipman cruise in July 1940, and spent his 21st birthday on the battleship USS Wyoming in Guantánamo Bay, Cuba.

After graduating from college, he completed three months of midshipman training on board the USS Prairie State.

[4] He saw action in both the Mediterranean and Pacific theaters, mostly aboard destroyers,[5] for which he was awarded both the Bronze and Gold stars.

[3] In 1961, after twelve years of practicing corporate law, Morgenthau accepted an appointment from President John F. Kennedy as United States Attorney for the Southern District of New York.

[3] After his defeat by the incumbent Governor Nelson Rockefeller, Morgenthau was reappointed U.S. Attorney and served in that position for the remainder of the Kennedy and Johnson administrations.

Morgenthau was less successful in raising funds and developing support than were two other candidates, Arthur Goldberg and Howard Samuels, and within weeks, he withdrew from the race.

[11] Eight men who were falsely arrested by New York City Transit Police officers in the scandal that shook the department were awarded more than $1 million in damages by a federal judge.

[12] Morgenthau retained a national profile while serving in what was technically a local office, in part because of his dogged pursuit of white-collar crime.

For the first time in decades, he encountered a vigorous primary opponent – former state court judge Leslie Crocker Snyder.

[14][15] Snyder won the endorsement of The New York Times, which, like virtually all of the city's establishment, had long supported Morgenthau.

[3] On February 27, 2009, Morgenthau announced that he would not seek re-election in 2009, saying: "I never expected to be here this long ... [R]ecently, I figured that I'd served 25 years beyond the normal retirement age.

[23][24] Cases which Morgenthau's office prosecuted include:[25] The character of District Attorney Adam Schiff (played by actor Steven Hill), the New York district attorney in the long-running TV series Law & Order from 1990 through 2000, was loosely based on Morgenthau.

[5][35] From 2021 through 2023, a fortysomething Robert Morgenthau was portrayed by actor Justin Bartha in seven episodes of the Epix series that takes place in the mid-1960s, Godfather of Harlem.