As Lord Keeper of the Privy Seal of Japan from 1940, Kido became one of the most influential advisors to Emperor Hirohito following the death of Saionji Kinmochi.

He recommended to Hirohito that Konoe succeed Mitsumasa Yonai for a second term as Prime Minister of Japan and was active with Konoe in the movement to replace the existing political parties with the Taisei Yokusankai (Imperial Rule Assistance Association) to form a single party state.

In 1941, Kido recommended that Hideki Tōjō become Prime Minister after Konoe's third term in office, as being one of the few people eligible who might be able to maintain control over more radical elements within the Imperial Japanese Army.

[citation needed] He also convinced the emperor that it would be necessary to deliver a personal speech in order to ensure that all civilians and soldiers would cease fighting.

He initially attempted to plead guilty in order to protect the emperor by taking all responsibility for imperial decisions advocating war unto himself.

In addition, Kido opposed the idea of continuing to punish war criminals under Japanese law after the end of the American Occupation.

According to his diary, "those called war criminals by the enemy's standards, especially those in responsible positions, were all performing loyal duties, and to punish them in the name of the emperor would be unbearable".