Klaus Bonhoeffer was born in Breslau, now Wrocław, Poland, to Karl Bonhoeffer, a professor of psychiatry and neurology, and his wife Paula (née von Hase), as their third son. His younger brother was the theologian Dietrich Bonhoeffer (February 4, 1906 – April 9, 1945). As a child, he went to the Grunewald-Gymnasium in Berlin with Hans von Dohnanyi.
He studied law at Heidelberg and received a doctorate for his thesis, "Workers' Committees as an Organ of the Workers' Coöperative" (Die Betriebsräte als Organ der Betriebsgenossenschaft). He also had further training in Berlin, at the University of Geneva, and in Amsterdam. On 3 September 1930, he wed Emmi Delbrück, who was Hans Delbrück's daughter, and Justus and Max Delbrück's sister.
In the years 1940 to 1944, he systematically forged contacts with various resistance groups working against the Nazi régime. Through his brother Dietrich, he had contacts with the church resistance, and through his brothers-in-law, Justus Delbrück, Hans von Dohnanyi and Rüdiger Schleicher, he had many contacts in the military resistance to Hitler, especially in the circle about Wilhelm Canaris in the Abwehr of the Oberkommando der Wehrmacht. Through his wife's cousin Ernst von Harnack, he was connected to the social-democratic resistance. Klaus Bonhoeffer also led his colleague Otto John, among others, into the resistance. He used his travel opportunities to further the cause against the Nazis.
According to the detention book kept at the Lehrter Straße prison in Berlin, where the Gestapo had a special section for political prisoners, Bonhoeffer was arrested on 1 October 1944 and sentenced to death at the German "People's Court" (Volksgerichtshof) on 2 February 1945. On the night of 22-23 April 1945, as Soviet troops were already reaching Berlin's eastern outskirts, he was taken forth by a special squad from the Reichssicherheitshauptamt and killed with a shot to the neck.
The only eyewitness to these murders was Herbert Kosney, who managed to move his head at the last moment so that the shot meant for his neck missed.