The story is centered around a young boy named Masaru Saiga, who inherits a massive fortune and aspires to become a puppeteer; Narumi Katō, a kung-fu expert who suffers from Zonapha syndrome (a strange illness that stops his breathing unless he makes people laugh); and Shirogane, a silver-haired woman and Masaru's caretaker who controls the puppet Harlequin.

Karakuri Circus was adapted into a 36-episode anime television series by Studio VOLN, broadcast from October 2018 to June 2019.

After 9 years of searching, Yin arrived in Quiberon, France, only to discover that Francine had fallen ill and had been imprisoned by fearful villagers.

In the hopes of curing and freeing her, Yin then worked to create the Aqua Vitae, an elixir of life that could impart incredible healing powers and a greatly increased lifespan.

Another 23 years passed and the younger brother Jin had created an automaton in her image and injected it with Aqua Vitae in hopes of bringing it to life.

When Lucille drank the water, she acquired Yin's memories and knowledge along with his puppet Harlequin, and she vowed to crush Jin's automata.

Years later, Shōji Saiga learned swordsmanship at Miura Dojo in Nagasaki while also studying to be a doctor under Dr. Bai Yin.

While treating a sick Mr. Nakayama, Shōji encountered a healing woman who called herself Tohno-dayu, although her real name was Angelina.

Angelina was mortally wounded by the automata and Shōji decided to keep Éléonore's existence a secret so he sent her to the Quiberon orphanage to be raised by Lucille.

Thirty-seven years later, Shōji visited the orphanage and found that Éléonore remembered him because of the memories of Francine transferred to her via the Aqua Vitae.

However Sadayoshi's plan was to leave his fortune to Masaru as bait to cause the destruction of the Kuroga clan.

The story starts when Masaru's father dies and leaves 18 billion yen of inheritance solely to him.

In the first arc, Narumi Katō joins the Shirogane to battle the automatons (auto-mannequins) and save the world from the Zonapha syndrome.

In the second arc, Éléonore and Masaru join the Nakamachi Circus and attempt to live a normal life as possible but their fates are still heavily linked to their pre-determined destiny.

[13][14] An official guidebook was published by Shogakukan under the Shōnen Sunday Comics Special imprint on July 16, 2004.

[19] In February 2021, Sentai Filmworks announced that they had licensed the series for home video and digital release.

The cast included Taiga Fukazawa as Masaru Saiga, Koudai Takikawa as Narumi Kato, Momoka Onishi and Riho Iida as Shirogane/Francine (double cast), Kairi Miura as Bai In, Ryōtarō Kosaka as Bai Jin, Kento as Eiryo Ashihana, Shōjirō Yokoi as George LaRoche, Yūki Ochi as Guy Christophe Rech, Ryōko Tanaka as Lucille Berneuil, Natsuki Maeda as Harlequin, Saki Endō as Fatima, Yōjirō Murata as Faceless, Mitsuru Karahashi as Pantalone, Hiroya Matsumoto as Arlecchino, Seshiru Daigo as Columbine and Shūhei Izumi as Dottore.

[38] On a 2020 poll conducted by the Goo website about the best Weekly Shōnen Sunday titles, Karakuri Circus ranked ninth.