Born in Stettin, Germany, Haupt was the son of Hans Max and Erna (Froehling) Haupt. Hans Haupt was a World War I Imperial German Army veteran who came to Chicago in 1923 to find work. His wife and son followed in 1925. Herbert Haupt became a United States citizen in 1930, at the age of 10, when his parents were naturalized. He attended Lane High School and later worked at the Simpson Optical Company as an apprentice optician.
In 1941, Herbert Haupt, with two friends, Wolfgang Wergin and Hugo Troesken, set off on a world trek. Troesken was turned back at the Mexican border for lack of proper identification, but Haupt and Wergin continued. Neither Haupt nor Wergin had been able to secure American passports before the trip. As they were German born (and thus still considered by Germany to be its citizens), they secured German passports from the Embassy in Mexico City. They sailed to Japan, where they found work on a German merchant ship bound for France. Haupt and Wergin arrived in France at the time of the Japanese attack on Pearl Harbor, following which Adolf Hitler had declared war against the United States. Now stranded in Europe, Haupt went to stay at his grandmother's home in Stettin. Wergin enlisted in the German Army (the Wehrmacht).
As a civilian coast watcher, Haupt was awarded an Iron Cross for having helped his passenger ship run the British blockade when he served as a lookout on the way to France. This drew the attention of the Abwehr (Secret Service), which recruited him to return to America as a saboteur. Haupt later insisted he accepted the job only as a way to return home.
Operation Pastorius consisted of 12 English-speaking Germans who were trained as secret agents at the Brandenburg Sabotage School. Eight eventually graduated and were sent to the United States via U-Boat to try to damage the US war industries. Haupt and three others landed on Ponte Vedra Beach, Florida on June 17, 1942. The remaining group landed on Long Island, New York. Haupt promptly took a train from Jacksonville to Chicago, where he stayed with his parents and visited his girlfriend. Haupt may well have intended to remain inactive until the end of the war. However, two members of the Long Island group, (George John Dasch and Ernst Peter Burger), had decided to defect to the Americans and did so almost immediately. They informed on their comrades. Haupt and his parents were arrested in Chicago on June 27.
Herbert Haupt and the other seven "U-Boat Raiders" were sent to Washington, D.C., where they faced a military tribunal. All were found guilty of being enemy agents, and even though they had not carried out any sabotage, six – including Haupt – were sentenced to death. Dasch and Burger received long prison sentences, which were commuted to deportation after the war.
Herbert Hans Haupt, Edward Kerling, Hermann Neubauer, Werner Thiel, Heinrich Heinck, and Richard Quirin were all executed on August 8, 1942 in the District of Columbia's electric chair. It was the largest mass execution by electrocution ever conducted.
Only 22 years old, Haupt broke down just before his execution. However, witnesses say he recovered and proceeded to "die like a real man" in the electric chair. It took Haupt seven minutes to die in the electric chair. His last undelivered letter to his father read, "Try not to take this too hard. I have brought nothing but grief to all of my friends and relatives who did nothing wrong, my last thoughts will be of Mother."
Haupt was buried with the five others in the Potter's Field in Blue Plains, D.C. The graves were originally marked by wooden boards with numbers, but eventually a small monument was placed over the graves in 1982. Government officials removed the monument, leaving those buried at Blue Plains in unmarked graves in a wooded, fenced-in area.
Haupt's parents were convicted of treason and stripped of their citizenship for not informing on their son. Haupt's mother, Erna Haupt, was released and deported to Germany in 1946. Hans Haupt, who had been sentenced to life imprisonment after appealing his conviction to the Supreme Court in 1943, was convicted again on June 9, 1944. He was finally released and deported in 1957. Unfortunately for them, their native city of Stettin had been transferred to Poland after World War II and its German population largely expelled. The Haupts had no home to return to.
In 2001, Herbert Haupt was in the news again as President Bush attempted to use military tribunals to try American citizens after the September 11, 2001, attacks. The Supreme Court ruling regarding Haupt, the only US citizen executed in the affair, was cited again. (Ex parte Quirin)