The forerunner of the Ministry of Foreign Affairs is the diplomatic institution established within the new Meiji government. In 1869, the government promulgated the Shokuinrei (Personnel Order), and fundamentally reformed the central structure. As a part of these reforms, the Ministry of Foreign Affairs was established under the Dajokan (Grand Council of State) with the Diplomatic Lord as its head.

In 1870, the following year, the system was for diplomatic missions established and commissioners were dispatched to four countries, the United Kingdom, France, Prussia and the United States of America. The first official embassy was established in the United Kingdom later in 1905.

After World War II, the Law for the Establishment of the Ministry of Foreign Affairs was established in 1951 and the Ministry bears the responsibility for a wide range of foreign policy including security policy, external economic policy, economic cooperation policy and international exchange policy.

Furthermore, the Final Report on the reform of the Ministry of Foreign Affairs was announced on March 27, 2003. The Ministry of Foreign Affairs is preparing to make the transition to a new organization beginning in FY2004, which aims to develop an organization that can carry out "dynamic and strategic diplomacy aimed toward the realization of Japan's safety and prosperity."