After World War II, Berlin was divided into the West, controlled by The United States, the UK, and France, and the East, controlled by the Soviet Union, resulting in a Cold War for decades. This bibliometric study analyzes the influence of the Cold War on pharmacological research in Berlin by evaluating publication patterns in Naunyn-Schmiedeberg’s Archives of Pharmacology from 1947 to 1974 (n = 383). The publications highlight the political disparities in scientific output, exacerbated by the founding of the Free University of Berlin (FUB) as a countermeasure to Soviet repression, promoting academic freedom in West-Berlin. Researchers in West-Berlin published many more papers in Naunyn-Schmiedeberg’s Archives of Pharmacology than researchers in East-Berlin and received much more citations. West-Berlin adopted English as a scientific language much more rapidly than East-Berlin. West-Berlin and East-Berlin focused on totally different research topics. This paper demonstrates how political freedom, financial support, and internationalization boosted research productivity in West-Berlin. In contrast, political suppression, financial scarcity, and restricted international ties hindered scientific development in East-Berlin.