During their discussion of a sensitive investigation A, the Fourth Raikage, and his subordinates are ambushed by a cloaked intruder. As the Kumogakure leader repels the assault, he is shocked to discover that the culprit is Naruto Uzumaki!

However, the assassination attempt is not the only crime attributed to the young ninja, who vigorously denies the accusations. To avoid a diplomatic conflict, Tsunade forcibly sends him to Kusagakure's Houzuki Castle—a maximum-security penitentiary dedicated to ninja criminals—until the situation is resolved.

Despite his powers being immediately suppressed by Mui, the prison's warden who possesses the ability to seal chakra, Naruto recklessly engages in futile escape attempts. But with the help of two fellow inmates, he realizes that there is more to this legendary detention facility than meets the eye. Uncovering a terrible secret, the trio embarks on a dangerous operation that may be Naruto's only chance to break free and prove his innocence.

Although it is debatable where Naruto: Shippuuden Movie 5 - Blood Prison is set in the timeline of the main series due to confusing story elements, it is likely to fall somewhere after episode 220 during the "Fourth Shinobi World War: Countdown" and "Paradise Life on a Boat" arcs.

The movie was released in theaters on July 30, 2011, earning 840 million yen in box office revenue. The DVD version was made available on April 27, 2012 in Japan. Neon Alley began streaming the film on January 26, 2014 and Viz Media released it on DVD and Blu-ray in North America on February 18, 2014.

While the previous movies were produced with the participation of the television series' screenplay writers, Naruto: Shippuuden Movie 5 - Blood Prison was entrusted to the mystery writer Akira Higashiyama. For this reason, "Shippuuden" was removed from the Japanese original title.