Stefan D. Pauly joined the German Navy in 1982. He began his career with the German Submarine force at Submarine Squadron 1. He commanded "Unterseeboot U-25" from 1991 through 1993 and served as the Commander of Submarine Squadron 3 from 2002 to 2004. Following command, he was appointed as Assistant Chief of Branch for Naval Operations in the Ministry of Defense Navy Staff, where he supported planning of national naval operations and German Navy contributions to multinational exercises and operations. From 2010 through 2013, he headed the Command and Control Group for Maritime Operations at the Bundeswehr Joint Forces Operations Command, where he was responsible for the mission-related coordination of maritime operations with allies and coalition partners.
He attended the Federal Armed Forces Command and Staff College from 1995 through 1997, focusing on national security decision-making, strategy and policy, joint and combined military operations and graduated from the German Capstone Course in 2015.
Ashore, Stefan has spent significant time in military intelligence. He served in the Intelligence Directorate at Fleet Command and consequently appointed as Section Head for Strategic Intelligence for NATO HQ SACLANT, Norfolk, Virginia, USA. He was also an analyst focusing on the Middle East and Northern Africa as part of the Joint Staff for the Federal Ministry of Defense. After completing a tour with the Federal Intelligence Service, Stefan became the Head of Naval Intelligence at the German Navy Headquarters in 2013, followed by an appointment to Branch Head for Military Intelligence for the Federal Ministry of Defense-General for Strategy and Operations. Afterwards Stefan was assigned as the Assistant Chief of Staff J2 at NATO HQ JFC Naples, where he directed the collection and processing of critical information regarding the operational environment in NATO's Strategic Direction South. In 2019, Stefan became the inaugural Chief of Staff for the newly formed Allied Joint Force Command Norfolk in Norfolk, Virginia, USA.
In June 2022, he was appointed Commander Surface Forces NATO and Deputy Chief of Staff Operation at NATO's Maritime Command in Northwood.