NANKI-POO, son of the Mikado of Japan, to escape the attentions of Katisha, an elderly Lady of his Father's Court, who is determined to marry him, runs away, and is touring the country as a strolling player. He arrives in Titipu, hoping to meet Yum-Yum, with whom he has fallen in love. He there learns the alterations in Ko-Ko's prospects, for instead of being a tailor under sentence of death for flirting, Ko-Ko has, by one of the eccentric decrees of the Mikado, been elevated to the rank of Lord High Executioner of Titipu, and is to marry his ward, Yum-Yum.
During the preparations for the wedding a letter arrives from His Majesty the Mikado complaining that no executions have taken place in Titipu for over a year, and threatening the degradation of the town and all officials, unless an execution takes place immediately.
Ko-Ko declines, as do also the other two Noble Lords, Pooh-Bah and Pish-Tush, to allow themselves to be beheaded for the good of the town; and while considering his dilemma, Ko-Ko is interrupted by Nanki-Poo, who has resolved to end his life, because of his hopeless love for Yum-Yum. An arrangement is entered into by which Nanki-Poo agrees to be beheaded in a month's time, on consideration of being allowed to marry Yum-Yum at once.
The joy of all is broken into by the arrival of Katisha, who claims Nanki-Poo as her future husband, and leaves in high dudgeon to inform the Mikado of the whereabouts of his truant son.
The Second Act opens with preparations for Yum-Yum's bridal. The happiness of Nanki-Poo and Yum-Yum is somewhat dashed by Ko-Ko, who explains that when a man is beheaded his wife is, by the Mikado's law, buried alive. The arrival of the Mikado so perturbs Ko-Ko that he hurries them off, saying that he will swear that he has beheaded Nanki-Poo, a statement borne out by Pooh-Bah and Pitti-Sing, whose confusion and dismay are complete when informed by the Mikado that Nanki-Poo is heir to the throne.
Ko-Ko, to remedy the unfortunate position into which he has blundered, makes violent love to Katisha, and offers himself as a substitute for Nanki-Poo as husband. She accepts, and interceding on behalf of all, a happy ending is consummated by the Mikado forgiving his son and welcoming his daughter-in-law.