The Pinafore, a "saucy" beauty of a ship in Her Majesty's navy is anchored in the harbour at Portsmouth. Its sailors are busy scrubbing the decks for the expected arrival of Sir Joseph Porter, K.C.B., Britain's First Lord of the Admiralty. "Little Buttercup", a bumboat woman comes aboard to sell to the sailors her stock of "snuff and tobaccy and excellent jacky," and other luxuries. A handsome and accomplished sailor, Ralph, tells his messmates that he is in love with the Captain's daughter, Josephine. Dick Deadeye reminds the starry-eyed seaman that Captain's daughters don't marry foremast hands! The Captain arrives to inspect his crew. The gentleman captain sings that he never uses foul language and is never sick at sea — well, "hardly ever."
 

Josephine is sought in marriage by Sir Joseph, but she is secretly in love with a lowly sailor: Ralph. It also seems that Little Buttercup has a romantic interest in the Captain and has a secret about Ralph! Sir Joseph arrives attended by his many "sisters and his cousins and his aunts," among whom is his loyal but jealous cousin Hebe. He explains that he rose to the top post in the Navy by sticking close to his desk and never going to sea. He also encourages the Captain to request that his sailors follow an order with the phrase "if you please." After all, his Lordship notes, "a British sailor is any man's equal." He presents the crew with a song that he himself has composed. Sir Joseph and the Captain retire below decks to discuss the proposed marriage.

Ralph finds Josephine alone on deck and declares his love for her and his willingness to try to fit in with middle-class society. She rejects his love, although his simple eloquence goes to her heart. She is a dutiful daughter and cannot forget the disparity in their ranks. But when Ralph threatens suicide, the lady relents and declares her love for him. With the crew, and the sisters, cousins, and aunts assisting, the lovers plot to elope that very night. Dick Deadeye warns the pair of the impropriety of their plan, but he is forced to retreat.

Later that night, Captain Corcoran is alone on deck with his guitar and sings to the moon of his troubles. Buttercup comes to him and reveals her affection. He tells her that because of his rank he can never be more to her than a friend; but she hints darkly that a change is in store for him, and "things are seldom what they seem." Sir Joseph returns, complaining that Josephine does not favor his suit. The Captain comforts him by theorizing that she is dazzled by his lofty station and suggests that he plead his cause on the ground that "love levels all ranks". When Josephine hears this argument, she considers how eloquently Sir Joseph has stated the justification for her to marry Ralph! Dick Deadeye finds the Captain alone and reveals the planned elopement. He and the Captain lie in wait for the crew, who steal in "carefully on tip-toe." The Captain confronts the elopers and is so exasperated that he actually swears, "Damme!", which is overheard by Sir Joseph Porter. Judging first and asking questions later, Sir Joseph orders the Captain to go to his cabin for this "ill-advised asperity."

Upon inquiry, Sir Joseph finds out that Ralph and Josephine love one another and orders the sailor to the brig. Affairs are interrupted by Buttercup, who discloses her long-concealed secret... and the story is brought to a swift conclusion.