Most security cooperation between the EU and Japan is non-military in nature. For Japan, military-to-military cooperation has a potential to further promote security cooperation between Japan’s Self-Defence Forces and European forces. Yet, Japan considers NATO rather than the EU as a primary military partner. For the EU, military cooperation with Japan promotes shared values enshrined in the CSFP, but the EU also aims to balance its strategic interests with China and Japan. The US remains a pivotal external actor shaping EU–Japan military cooperation. Existing military cooperation is mainly confined to the Indian Ocean and the Gulf of Aden and, it is suggested, this is indicative of the likely pattern of future military cooperation. The ability of either partner to influence security in each other’s respective region is limited but the Strategic Partnership Agreement, agreed in 2017, will permit more extensive cooperation, including Japan’s direct involvement in CSDP operations. Further bilateral cooperation with EU members, some of it in the South China Sea, should not be ruled out; nor should defence industrial cooperation although, from a Japanese standpoint, it remains a fiercely competitive export market.