Kogon was born in Munich, the son of a Russian diplomat. He spent the larger portion of his youth in Catholic cloisters. After studying national economy and sociology at university in Munich, Florence and Vienna, Kogon received his doctorate in 1927 in Vienna with a dissertation on the "Cooperative State of Fascism" (Kooperativstaat des Faschismus). That same year, Kogon got a job as editor of a Catholic magazine, Schönere Zukunft ("Brighter Future") and stayed there till 1937. Through his work, he made the acquaintance of sociologist Othmar Spann, who recommended him for the "Central Committee of Christian Unions" (Zentralkommission der christlichen Gewerkschaften). Kogon was an advisor there several years later. In 1934, after the July Putsch, Kogon took over the asset management of the House of Saxe-Coburg and Gotha.

An avowed opponent of Nazism, Kogon was arrested by the Gestapo in 1936 and again in March 1937, charged with, among other things, "work[ing] for anti-national socialist forces outside the territory of the Reich". In March 1938, he was arrested a third time and in September 1939, he was deported to Buchenwald, where he spent the next six years as "prisoner number 9093".

At Buchenwald, Kogon spent part of his time working as a clerk for camp doctor Erwin Ding-Schuler, who headed up the typhus experimentation ward there. According to Kogon's own statements, he was able to develop a relationship bordering on trust with Ding-Schuler, after becoming his clerk in 1943. In time, they had conversations about family concerns, the political situation and events at the front. According to Kogon, through his influence on Ding-Schuler, he was able to save the lives of many prisoners. In early April 1945, Kogon and the head prisoner nurse in the typhus experimentation ward, Arthur Dietsch found out from Ding-Schuler that their names were on a list of 46 prisoners who the SS wanted to execute shortly before the expected liberation of the camp. Ding-Schuler saved Kogon's life at the end of the war by hiding him in a crate and smuggling him out of Buchenwald.

Right after being liberated in 1945, Kogon again began working as a journalist. He worked as a volunteer historian for the United States Army at Camp King and began writing his book, Der SS-Staat — Das System der deutschen Konzentrationslager ("The SS-State — The System of the German Concentration Camp"), first published in 1946 and is still stands as the basic reference on Nazi crimes. The book was translated into several languages. The German language version alone sold 500,000.

Despite this intensive involvement with the past, Kogon primarily chose to look ahead, toward building a new society - one that would blend with Kogon's convictions of Christianity and socialism. Kogon had already spoken about his ideas in Buchenwald with fellow prisoner Kurt Schumacher. However, the rapid growth of the Social Democratic Party hindered the proposed alliance of right-wing social democrats and the Centre Party into a "Labour Party" after the British model.

In September 1945, Kogon and other journalists, among them, Walter Dirks, later his friend and companion, published the Frankfurter Leitsätze ("Frankfurt Guiding Principles"). In this Program of the Volkspartei ("popular party"), they called for an "economic socialism on a democratic basis", laying out an important basis for the Christian-socialist founding program of the Hessian Christian Democratic Union (CDU), also for the Constitution of Hesse, which was finalized at the end of 1946 and provided for the nationalization of key industries.

In 1946, Kogon and Dirks founded the Frankfurter Hefte ("Frankfurt Notebooks"), a cultural and political magazine with a left-wing Catholic point-of-view. They quickly reached a circulation of 75,000, which was very high for that time and until 1984, remained one of the most influential socio-political and cultural magazines in the postwar era. In the Gesellschaft Imshausen, Kogon was involved in the search for a "third way" in the renewal of Germany. He quickly turned away from Konrad Adenauer's CDU, which was not interested in communal ownership and nationalization of key industries. Kogon instead wrote many essays taking a critical look at the Adenauer government. Among other issues, he turned against the Wiederbewaffnung, atomic weapons and the "madness of excessive armament".

As a lesson from Nazism, Kogon early called for departure from a traditional nation-state and fought for the establishment of a European Republic. Among others, he was involved in the Union of European Federalists (UEF) and the German section of the UEF, where he served as the first President from 1949 to 1954. From 1951 to 1953, Kogon was also president of the German council of the European Movement.

Alfred Grosser counted him as one of the three "creators of Europe".

Kogon was appointed professor of the newly established chair for political science at the Technische Universität Darmstadt In 1951, teaching there till his retirement in 1968, whereupon he was made professor emeritus. University president Johann-Dietrich Wörner later attested to Kogon's importance, saying, "He shaped the moral conscience of the university to the present day." From January 1964 to January 1965, Kogon headed the political magazine, "Panorama", broadcast by the German station, ARD. He began serving as the program's moderator in March 1964.

Later, Kogon supported the Eastern policy of the Socialist-Liberal coalition and actively promoted the reconciliation of Poland with the Soviet Union. The state of Hesse honored Kogon in 1982 with the newly created Hessian Culture Prize. His final years were spent in quiet retirement Königstein im Taunus, where there is now a street named for him. In 2002, the city began awarding an annual "Eugen Kogon Prize for Democracy in Action". The first winner was the former Polish Foreign Minister Wladyslaw Bartoszewski.

• Der SS-Staat. Das System der deutschen Konzentrationslager, Alber, Munich (1946) Numerous subsequent editions, most recently by Heyne, Munich (1995) ISBN 3-453-02978-X
• Gesammelte Schriften in 8 Bänden. Beltz, Weinheim 1995—1999
• 1. Ideologie und Praxis der Unmenschlichkeit (1995) ISBN 3-88679-261-7
• 2. Europäische Visionen (1995) ISBN 3-88679-262-5
• 3. Die restaurative Republik (1996) ISBN 3-88679-263-3
• 4. Liebe und tu was du willst (1996) ISBN 3-88679-264-1
• 5. Die reformierte Gesellschaft (1997) ISBN 3-88679-265-X
• 6. Dieses merkwürdige wichtige Leben (1997, ISBN 3-88679-266-8
• 7. Bedingungen der Humanität (1998) ISBN 3-88679-267-6
• 8. Die Idee des christlichen Ständestaats (1999) ISBN 3-88679-268-4

Works as co-editor

• Kurt Fassmann with contributions by Max Bill, Hoimar von Ditfurth and others (Editors), Die Großen - Leben und Leistung der sechshundert bedeutendsten Persönlichkeiten unserer Welt. Kindler Verlag, Zurich (1977)
• Eugen Kogon, Hermann Langbein, Adalbert Rückerl and others (Editors), Nationalsozialistische Massentötungen durch Giftgas. Fischer-Verlag, Frankfurt am Main (1986) ISBN 3-596-24353-X