Emperor Meiji, much loved by the Japanese, moved the capital of Japan to Tokyo. He was largely responsible for the modernization of Japan and for making it a major international economic power.
After his death in 1912, the Japanese parliament approved a resolution to commemorate his importance with a shrine, and the choice fell to an iris garden Emperor Meiji and his wife frequently visited.
Let me leave you with an interesting fact: the shrine does not contain the tomb of the Emperor, which is in Fushimi Momoyama, south of Kyoto.