Werder Bremen striker Yuya Osako scored a hat trick, while Liverpool midfielder Takumi Minamino — who is currently on loan at Southampton — was also on the scoresheet.
Mongolia, who are ranked No. 190 in the world, registered just two shots compared to Japan’s 34.
It is Japan’s second-biggest win, only behind a 15-0 win over the Philippines in 1967.
The win means Japan will advance to the next phase of Asia’s qualifying tournament for the World Cup if they defeat Myanmar when the teams meet on June 3.
Having gone into the halftime break five goals to the good, the second period saw a further nine goals for the Samurai Blue — including four inside just 11 minutes.
Japan’s other scorers included Daichi Kamada, Hidemasa Morita, Takuma Asano, an own goal by Khash Erdene Tuyaa and braces from Sho Inagaki, Junya Ito and Kyogo Furuhashi.
Despite nominally being a home match for Mongolia, the game took place in an empty Fukuda Denshi Arena in Chiba, Japan, after Mongolia had to give up hosting rights due to quarantine regulations.
It wasn’t the first one-sided result of the week as on Monday, Canada beat the Cayman Islands 11-0 in another World Cup qualifier.