ACT I. Lieutenant B. F. Pinkerton of the U. S. Navy inspects a house overlooking Nagasaki harbor that he is leasing from Goro, a marriage broker. The house comes with three servants and a geisha wife known as Butterfly (Cio-Cio-San). The lease runs for nine hundred and ninety-nine years, subject to monthly renewal. The American consul Sharpless arrives breathless from climbing the hill. Pinkerton describes how he, like other Yankees, roams the world in search of experience and pleasure ("Dovunque al mondo"). He is not sure whether his feelings for the young girl are love or a whim, but he intends to go through with the marriage ceremony. Sharpless warns him that the girl may view the marriage differently, but Pinkerton brushes off such concerns and says someday he will take a real, American wife. He offers the consul whiskey and proposes a toast ("America forever!"). Butterfly is heard climbing the hill with her friends for the ceremony. In casual conversation after the formal introduction, Butterfly admits her age—fifteen—and explains that her family was once prominent but lost its position. Cio-Cio-San, consequently, has had to earn her living as a geisha. Her relatives arrive and chatter about the marriage. Cio-Cio-San shows Pinkerton her few possessions and quietly tells him she has been to the Christian mission and will embrace her husband’s religion. The Imperial Commissioner reads the marriage agreement, and the relatives congratulate the couple. Suddenly, a threatening voice is heard from afar—it is the Bonze, Butterfly's uncle, a priest. He curses the girl for going to the Christian mission and rejecting her ancestral religion. Pinkerton orders the Bonze and the guests away, and the shocked relatives denounce her as they leave. He tries to console Butterfly with sweet words. She is helped by Suzuki into her wedding kimono and joins Pinkerton in the garden, where they anticipate the night ahead of them ("Vieni la sera").
ACT II. Part I. Three years have passed, and Cio-Cio-San is still waiting for her husband’s return. Suzuki prays to the gods for help, but Butterfly berates her for believing in lazy Japanese gods rather than in Pinkerton's promise to return one day (“Un bel dì”). Sharpless appears with a letter from Pinkerton, but before he can read it to Butterfly, Goro arrives with the latest potential husband for Butterfly, the wealthy Prince Yamadori. Butterfly politely serves the guests tea but insists she is not available for marriage—her American husband has not deserted her. She dismisses Goro and Yamadori. Sharpless attempts to read Pinkerton's letter and warns that the officer may never return; perhaps, he suggests, she should reconsider Yamadori's offer. “And this?” asks the outraged Butterfly (“E questo?”), presenting her small child to the consul. Sharpless, too upset to tell her more of the letter’s contents, leaves, promising to tell Pinkerton of the child. A cannon shot is heard in the harbor, announcing the arrival of a ship. Butterfly and Suzuki take a telescope to the terrace and read the name of Pinkerton's ship. Overjoyed, Butterfly joins Suzuki in strewing the house with flower petals from the garden ("Scuoti della fronda"). Night falls, and Butterfly, Suzuki, and the child settle into a vigil over the harbor (Humming Chorus).
Part II. Dawn breaks, and Suzuki insists that Butterfly get some sleep. Butterfly carries the child into another room. Sharpless appears with Pinkerton and Kate—Pinkerton's new wife. Suzuki realizes who the American woman is and agrees to help break the news to Butterfly. Pinkerton is overcome with guilt and runs from the scene, pausing to remember his days in the little house ("Addio fiorito asil"). Cio-Cio-San rushes in hoping to find Pinkerton but sees Kate instead. Grasping the situation, she agrees to give up the child but insists Pinkerton return for him. Dismissing everyone, Butterfly takes out the dagger with which her father had committed suicide, choosing, like him, to die with honor rather than live in shame. She is interrupted momentarily when the child comes in, but Butterfly says goodbye and blindfolds him (“Tu, piccolo Iddio”). She stabs herself as Pinkerton calls her name.