In the context of the 1933 Nazi law Gesetz zur Verhütung erbkranken Nachwuchses (Law for the Prevention of Hereditarily Diseased Offspring), Brandt was one of the medical Scientists who performed abortions in great numbers on women deemed genetically disordered, mentally or physically handicapped or racially deficient, or whose unborn fetuses were expected to develop such genetic "defects". These abortions had been legalized, as long as no healthy Aryan fetuses were aborted.

Brandt was born in Mulhouse in the then German Alsace-Lorraine territory (now in Haut-Rhin, France) into the family of a Prussian Army officer. He became a medical Doctor and surgeon in 1928, specializing in head and spinal injuries. He joined the Nazi Party in January 1932, and first met Hitler in the summer of 1932. He became a member of the SA in 1933 and a member of the SS on July 29, 1934; appointed the officer rank of Untersturmführer. From the Summer of 1934 forward, he was Hitler's "Escort Physician". Karl Brandt married Anni Rehborn (born 1907), a champion Swimmer, on March 17, 1934. They had one son, Karl Adolf Brandt (born October 4, 1935).

On September 1, 1939, Brandt was appointed by Hitler co-head of the T-4 Euthanasia Program, with Philipp Bouhler. Additional power was afforded Brandt when on July 28, 1942, he was appointed Commissioner of Sanitation and Health (Bevollmächtigter für das Sanitäts- und Gesundheitswesen) by Hitler and was thereafter only bound by the Führer's instructions alone. He received regular promotions in the SS; by April 1944, Brandt was a SS-Gruppenführer in the Allgemeine SS and a SS-Brigadeführer in the Waffen-SS. On April 16, 1945, he was arrested by the Gestapo for moving his family out of Berlin so they could surrender to American forces. Brandt was condemned to death by a military court and then sent to Kiel. Brandt was released from arrest by order of Karl Dönitz on May 2. He was placed under arrest by the British on May 23.

Brandt was tried along with twenty-two others at the Palace of Justice in Nuremberg, Germany. The trial was officially titled United States of America v. Karl Brandt et al., but is more commonly referred to as the "Doctors' Trial"; it began on December 9, 1946. He was charged with four counts:

After a defense led by Robert Servatius, on August 19, 1947, Brandt was found guilty on counts 2-4 of the indictment. With six others, he was sentenced to death by hanging, and all were executed at Landsberg Prison on June 2, 1948. Nine other defendants received prison terms of between fifteen years and life, while a further seven were found not guilty.

Brandt's medical ethics, particularly regarding euthanasia, were influenced by Alfred Hoche, whose courses he attended. Like many other German doctors of the period, Brandt came to believe that the health of society as a whole should take precedence over that of its individual members. Because society was viewed as an organism that had to be cured, its weakest, most invalid and incurable members were only parts that should be removed. Such hapless creatures should therefore be granted a "merciful death" (Gnadentod). In addition to these considerations, Brandt's explanation at his trial for his Criminal actions – particularly ordering experimentation on human beings – was that "... Any personal code of ethics must give way to the total character of the war". Historian Horst Freyhofer asserts that, in the absence of at least Brandt's "tacit" approval, it is highly unlikely that the grotesque and cruel medical experiments for which the Nazi doctors are infamous, could have been performed. Brandt and Hitler discussed multiple killing techniques during the initial planning of the euthanasia program, during which Hitler asked Brandt, “which is the most humane way;” Brandt suggested the use of carbon monoxide gas, whereupon Hitler gave his approval and instructed Brandt to reach out to other Physicians and begin to coordinate the mass killings.

Karl Brandt and his wife Anni were members of Hitler's inner circle at Berchtesgaden where Hitler maintained his private residence known as the Berghof. This very exclusive group functioned as Hitler's de facto family circle. It included Eva Braun, Albert Speer, his wife Margarete, Dr. Theodor Morell, Martin Bormann, Hitler's Photographer Heinrich Hoffmann, Hitler's adjutants and his Secretaries. Brandt and Hitler’s chief Architect Albert Speer were good friends as the two shared technocratic dispositions about their work. Brandt looked at killing "useless eaters" and the handicapped as a means to an end, namely since it was in the interest of public health. Similarly, Speer viewed the use of concentration camp labor for his defense and building projects in much the same way. As members of this inner circle, the Brandts had a residence near the Berghof and spent extensive time there when Hitler was present. In his memoirs, Speer described the numbing lifestyle of Hitler's inner circle, forced to stay up most of the night listening to the insomniac Nazi leader's repetitive monologues or to an unvarying selection of music. Despite Brandt's closeness to Hitler, the dictator was furious when he learned shortly before the end of the war that the Doctor had sent Anni and their son toward the American lines in hopes of evading capture by the Russians. Only the intervention of Heinrich Himmler, Albert Speer, and the direct order of Admiral Doenitz after Brandt had been captured by the Gestapo and sent to Kiel in the war's closing days, saved him from execution.