In 1929, nine year-old Sakamoto Chiyo and her sister are sold by their father to work within the entertainment districts of Kyoto. They are taken from their home in a coastal fishing village known as Yoroido and travel to Kyoto by train. Chiyo is taken to the Nitta okiya (geisha boarding house) in Gion to become a geisha, but her sister is taken to a brothel within Kyoto's pleasure district.
Chiyo is introduced to Auntie, Mother, and Granny. Both Auntie and Mother are strict, though Auntie is kinder to Chiyo, whereas Mother is driven by money and business. Chiyo is also introduced to Hatsumomo, the premier geisha of the okiya, its primary earner, and one of the most famous geisha of Gion, and Pumpkin, another maid at the okiya. Hatsumomo dislikes Chiyo and goes out of her way to torment her. When Chiyo fails an attempt to run away with her sister, Mother refuses to continue investing in Chiyo's future as a geisha.
A few years later, Chiyo is given money and a handkerchief in the street by a kind stranger known to Chiyo as the Chairman. Soon afterwards, Pumpkin prepares to make her debut as a maiko and the "younger sister" of Hatsumomo, whilst Chiyo remains a maid. Mameha, another famous geisha in Gion, persuades a reluctant Mother to reinvest in Chiyo's training, with Mameha acting as Chiyo's mentor and "older sister".
Chiyo becomes an apprentice geisha with the given name of Sayuri, and is reacquainted with Chairman Iwamura, his closest friend and business partner Nobu, and a number of other prominent men. As Sayuri gains popularity, Hatsumomo tries to hurt Sayuri's reputation and career in the hopes of Mother adopting Pumpkin as her heir instead.
Mameha orchestrates a bidding war for Sayuri's mizuage and uses the record-breaking payment for Sayuri's mizuage to cover all of her debts. Mother adopts Sayuri, and Hatsumomo begins a downward spiral into alcoholism before being thrown out of the okiya.
In 1944, geisha districts are ordered to close due to the ongoing war, and Sayuri desperately asks Nobu for help to avoid being conscripted into factory work. He sends Sayuri far north to live with his old friend, Arashino, where she stays for much of the war.
At the end of the war, Nobu visits Sayuri, asking that she return to Gion. Sayuri finds Pumpkin working in a new okiya; despite hoping to rekindle their friendship, Pumpkin later sabotages Sayuri's plan to scare Nobu off from proposing to be her danna, as revenge for taking her place in the adoption so many years ago.
A few days after her plan fails, Sayuri is summoned to meet the Chairman at a teahouse. She confesses that she has worked for years to become close to the Chairman. The Chairman admits that he has always known she was the girl he met on the street, and confesses his feelings for her as well, but felt he owed Nobu – his oldest and closest friend – the chance to be with Sayuri out of kindness. He also admits to having asked Mameha to train Sayuri.
Sayuri peacefully retires from geisha work when the Chairman becomes her danna. Sayuri relocates to New York City and opens her own small tea house for entertaining Japanese men on business in the United States. The Chairman remains her danna until his death.
