Some were burned alive with gasoline, or drowned, while others were buried alive or buried to their waists to be used for bayonet practice. According to the judgment of the International Military Tribunal for the Far East, also known as the Tokyo Trial in 1948, "Even girls of tender years and old women were raped in large numbers throughout the city, and many cases of abnormal and sadistic behaviour in connection with these rapings occurred. Many women were killed after the act and their bodies mutilated. Approximately 20,000 cases of rape occurred within the city during the first month of the occupation." Many Japanese soldiers described these horrific scenes and their actions in diaries, and some even took photographs.

Prior to the fall of Nanking, all foreign citizens were ordered to evacuate by their respective embassies and institutions. Despite the approaching siege, however, a few Westerners decided to remain behind and to try to protect Chinese civilians. This group of Westerners, composed of missionaries, doctors, nurses, journalists, educators, administrators and businessmen, established the International Committee for the Nanking Safety Zone and the International Red Cross of Nanking. On numerous occasions, they risked their lives by intervening to prevent the execution of Chinese men or the rape of women and young girls. Along with these selfless Westerners, a number of Chinese volunteers also risked their own safety to aid their fellow Chinese in the Safety Zone.  

In 1948, the Tokyo Trial convicted Iwane Matsui, commander of Japanese Imperial forces in central China, of Class B and Class C war crimes and sentenced him to death for responsibility over the Nanking Massacre.