In June 1869, by decree of Emperor Meiji, the Tokyo Shokonsha (Tokyo Shrine for Summoning Spirits) was established on Kudanzaka hill in Tokyo to commemorate imperial loyalists who died in the Boshin War. Omura Masujiro played a central role in selecting the site and designing the facility. In 1879 it was renamed Yasukuni Shrine — 'peaceful country.' War dead from subsequent conflicts including the Satsuma Rebellion, Sino-Japanese War, Russo-Japanese War, World War I, and World War II were progressively enshrined, eventually totaling approximately 2.46 million souls. Bakumatsu loyalists including Yoshida Shoin and Takasugi Shinsaku are among those enshrined, and Yasukuni has served as Japan's central national war memorial ever since.

On November 21, 1975, Emperor Showa visited Yasukuni Shrine — his last visit ever. Having visited eight times in the postwar era, this visit was offered in prayer for peace. However, when fourteen Class-A war criminals were secretly enshrined in October 1978, the Emperor reportedly expressed deep displeasure and never returned. According to the diary of Chamberlain Irie Sukemasa, the Emperor said: 'That is why I have not visited since then. That is my heart.' This decision has been maintained by the current Emperor as well, making the 1975 visit the start of the ongoing tradition of imperial non-attendance at Yasukuni. Nearly half a century after Emperor Showa's final visit, no reigning emperor has returned.

On October 17, 1978, during the autumn grand festival of Yasukuni Shrine, fourteen Class-A war criminals from World War II were secretly enshrined alongside the other war dead. Class-A criminals were war leaders convicted of 'crimes against peace' by the International Military Tribunal for the Far East (Tokyo Trials), including former Prime Minister Tojo Hideki and six others who were executed. The enshrinement was decided by Chief Priest Matsudaira Nagayoshi and was initially kept secret, only becoming public in 1979 when media reported it. Emperor Showa reportedly expressed deep concern and ceased all visits to Yasukuni from 1978 until his death, as revealed by an aide's diary released years later. This enshrinement transformed official visits by Japanese prime ministers and cabinet ministers into a major diplomatic and constitutional issue — drawing sharp protests from China, South Korea, and others — a controversy that remains unresolved today.