Act I
Outside a house in turn-of-the-century Nagasaki, Benjamin Franklin Pinkerton, an American naval officer and admitted Yankee vagabond, arranges with Goro to lease a residence for himself and his new bride, Cio-Cio-San, also called Butterfly. He is then introduced to Butterfly's servants, one of whom is Suzuki. While talking to Sharpless, the American consul, Pinkerton reveals that he purchased his bride for a hundred yen and that he can bow out of the marriage contract whenever he wishes. Sharpless tries to warn the officer that his teenage bride could really love him, but Pinkerton ignores the consul, drinking to the day when he will marry an American. Butterfly arrives with friends and relatives, greets Pinkerton, and shows him her paltry belongings, including the dagger her father used to kill himself. She confides to Pinkerton that she secretly converted to Christianity the day before so that she could worship the same God as her husband, for whom she is willing to forget her own people.

As they celebrate their wedding, the Bonze, Butterfly's devout uncle, storms in. He found out that she converted and denounces her for abandoning her faith and her family. They renounce her, and Pinkerton, visibly annoyed, demands that they all leave. Night falls and Butterfly joins Pinkerton outside, where she rapturously confesses her love. He leads her into the house.

Act II
Three years have passed since Pinkerton sailed for America. The devoted Butterfly tells Suzuki that one day soon they shall see Pinkerton's ship enter the harbor. Sharpless, who knows that Pinkerton and his new wife will soon arrive in Nagasaki, tries to persuade Butterfly to marry Prince Yamadori, but she refuses to listen. She shows the American consul the son that she has borne Pinkerton, convinced that her husband would never abandon her or his own child. The harbor cannon announces the arrival of Pinkerton's ship, and an elated Butterfly prepares for his imminent arrival.

Butterfly, her son, and Suzuki wait all night for Pinkerton, who finally appears the next morning with Sharpless and his new wife, Kate. Butterfly is resting, so Suzuki meets them. Suddenly overwhelmed by remorse, Pinkerton leaves because he cannot face the wife he abandoned. While Kate asks Suzuki to explain to Butterfly that Pinkerton's son would be better off in America, Butterfly awakens and emerges, seeing the strange woman in her garden. Sharpless tells her that the woman is Pinkerton's wife. Distraught, Butterfly retreats to the house to stab herself with her father's dagger. She parts sorrowfully from her son. When Pinkerton rushes into the room, it is too late to save her.