The kidnapping of Charles Lindbergh Jr. occurred on the evening of 1 March 1932. A $50,000 ransom was paid, but the infant was not returned. A corpse identified as the boy's was found on 12 May 1932 in the woods four miles from the Lindbergh home. The cause of death was listed as a very severe blow to the head.

More than two years later, on 18 September 1934, a gold certificate from the ransom money was discovered; it had a license plate number written on it. Gold certificates were rapidly being withdrawn from circulation; to see one was unusual and in this case, anything, attracted attention. The New York license plate belonged to a dark blue Dodge sedan owned by Hauptmann. Hauptmann was arrested the next day and charged with the murder.

The trial attracted wide media attention and was dubbed the “trial of the century.” Hauptmann was also named "The Most Hated Man In The World." The trial was held in Flemington, New Jersey and ran from 2 January to 13 February 1935. Col. Henry S. Breckinridge was Lindbergh's lawyer throughout the case and acted as intermediary in the ransom negotiations, assisted by Robert H. Thayer. (On discovering his missing child, Lindbergh phoned Breckinridge before calling the police.)

Evidence produced against Hauptmann included over $14,000 in ransom money that was found in his garage, a hand-made ladder supposedly used in the kidnapping (which matched wood and carpentry equipment found in his home), and testimony alleging handwriting and spelling similarities to that found on the ransom notes. Hauptmann was positively identified as the man to whom the ransom money was delivered. Other witnesses testified that it was Hauptmann who had spent some of the Lindbergh gold certificates, that he had been seen in the area of the Hopewell estate on the day of the kidnapping, and that he had been absent from work on the day of the ransom payment. Based on this strong but circumstantial evidence, Hauptmann was convicted and sentenced to death. He denied his guilt to the very end, insisting the box found to contain gold certificates had been left in his garage by a friend, named Isidor Fisch, who had returned to Germany and died there in March 1934.

New Jersey Governor Harold G. Hoffman (who later became infamous for embezzlement) secretly visited Hauptmann in his death row cell on the evening of 16 October 1935 with Anna Bading, a stenographer and fluent speaker of German. Hoffman urged the other members of the New Jersey Court of Errors and Appeals, then the state's highest court, to visit Hauptmann.

Despite Governor Hoffman's evident doubt as to Hauptmann's guilt, Hoffman was unable to convince the other members of the Court of Errors to re-examine the case, and on 3 April 1936 Hauptmann was executed in the electric chair at New Jersey State Prison known as Old Smokey. Hauptmann had requested a last meal consisting of celery, olives, chicken, french fries, buttered peas, cherries and cake. Reporters present at the execution reported that he went to the electric chair without saying any last words, but other reports later said that he was vehemently protesting his innocence.

After the execution, Hauptmann's widow, Anna, applied for and received special permission that was required to take her husband's body out of state, so that it could be cremated at the U.S. Crematory, also called the Fresh Pond Crematory, in the Maspeth neighborhood of Queens, New York. The memorial service there was religious (two Lutheran pastors conducted the service in German), and private (under New Jersey law public services were not permitted for felons, and Hauptmann's wife had agreed to this as a condition of receiving her husband's body) and was attended by only six people (the legal limit under New Jersey rules) but a crowd of over 2,000 gathered outside anyway. Hauptmann's widow had planned to return to Germany with the ashes.