The Naruto universe is filled with an amazing cast of characters, especially its villains. Far from the typical one-dimensional approach to good and evil, these villains possessed strong philosophies and ambitions about justice and morality. Sometimes, fans wanted to root for the villain just as much as the hero, and many times the villain even ended up saving the day and helping the heroes.
Looking at the major Naruto villains (excluding the Boruto series), there were incredible feats of unique kekkei genkais and fan-favorite jutsu but strength doesn’t always equal intelligence.
Updated by Amanda Bruce on August 26, 2021: Not all of the villains in the Naruto franchise are created equal. Fans have their favorites, but their favorites aren't necessarily the smartest of the bunch. From Akatsuki members to political schemers, the Naruto villains are a diverse bunch. Some of them excel in strategy, and those are largely the most intelligent.
Kakuzu
Like most of the Akatsuki members, Kakuzu was a missing-nin who had a bloodthirsty streak. Kakuzu was hardly the best strategist of the Akatsuki, but his method for prolonging his life required him to know the ins and outs of shinobi anatomy and chakra flawlessly.
Kakuzu was able to use the organs of those he killed in combat to replace his own, making him virtually immortal. He was a master at understanding when he could afford to sacrifice a heart (or two) in a fight, and when to leave to fight another day. It took multiple skilled shinobi teams to eventually bring him down.
Sasori
Another member of the Akatsuki, Sasori was a suitably creepy villain in Naruto for fans to watch in action. A master at puppetry, his puppets didn't even have to be created from wood for him to master them, which is where his particular brand of intelligence and skill came in.
Sasori was able to puppet dead bodies, making them last for much longer than they should. An arc in the anime saw him face off against the always analytical Sakura Haruno, and while she could pick out patterns in his methods, she couldn't defeat him alone.
The Sand Siblings
When Naruto introduced Gaara, Kankuro, and Temari of Sunagakure to the audience, it was as a trio of antagonists. The siblings were groomed by others to play a role in disrupting Konohagakure's peace without truly understanding the consequences at the time. That doesn't mean they aren't all very smart.
Gaara, after all, becomes the leader of his people as a teenager. The trio also train the next generation of shinobi before they're even done studying themselves. Temari also has the honor of being one of the few characters in the franchise who can even keep up with Shikamaru Nara's leaps of logic and strategic plans, nearly beating him in the Chunin Exams.
Rasa
Rasa wasn't the most empathetic of leaders in the shinobi world, and he took his turn as one of the Naruto bad guys before seeing the error of his ways, like a lot of the men who achieved great power in the franchise. He led the Village Hidden in the Sand, and Rasa was the man responsible for manipulating his children into initially being so hostile toward the Konohagakure villagers.
He raised his children - and instilled in his shinobi - a culture of violence and intimidation. Rasa was smart enough to use one of his own relatives to seal a tailed-beast inside, however, knowing he could control his own child's actions better than a stranger, and knowing how close of an eye he could have his advisors keep on Gaara. It was a cruel act, but not a dumb one.
Hidan
Hidan doesn't always seem like the most intelligent of the Akatsuki. He certainly doesn't have the knack for long-term planning that Pain or Tobi do, for example. Hidan does, however, much like Kakuzu, have a great understanding of anatomy and just how shinobi abilities work. That's how he manages to keep himself functionally immortal. That gives him an edge in a fight even when he isn't using his head for strategy.
What's interesting about him is that, despite not being a master strategist, he's able to keep up with Shikamaru in their initial battle. He's even able to quickly analyze and figure out how to stay one step ahead of him - with Kakuzu's help, of course. Ultimately, however, Shikamaru is able to outmatch him, which is why Hidan doesn't exactly outrank too many of the franchise villains.
Nagato Uzumaki/Pain
Despite being immobile and frail due to his battle with Hanzo, Nagato secretly created the alias of Pain and his Six-Paths bodies to carry out his plan to bring peace to the ninja world and during this time, only Konan and Tobi were aware of his disguise.
Pain guided the Akatsuki into a renowned group of international S-Rank rogue ninjas and successfully extracted all of the tailed beasts, except the Kyuubi. Before his death, Nagato strategically used Rinne Rebirth to revive those killed in the "Pain's Assault" arc (one of the longest and most destructive arcs in the Naruto anime), which stalled Tobi’s plan to resurrect Madara.
Kaguya Otsutsuki
As the progenitor of chakra on Earth, an Otsutsuki clan member, and the original jinchuriki of the Ten-Tails, Kaguya possessed unique knowledge and abilities not even shared by her son Hagoromo who was the Sage of Six Paths and the founder of Ninshu.
In spite of her profound expertise, Kaguya would be defeated by both her sons Hagoromo and Hamura and their reincarnates Naruto and Sasuke centuries later. However, she still possessed the incredible foresight to create Black Zetsu who would seed every major conflict in the franchise. That foresight alone makes her one of the smartest villains in Naruto.
Kurama/Kyuubi
Kurama was the strongest of the tailed beasts created by Hagoromo and as a witness to the evolution of Ninshu for a millennium, Kurama possessed immense knowledge of both chakra and humankind.
While Kurama was introduced as the nine-tailed demon fox who destroyed Konoha and spent most of the series trying to kill Naruto, he eventually became a key battle partner and advisor to Naruto and saved his life through quick-thinking numerous times.
Obito Uchiha/Tobi
Obito donned the guises of both Tobi and Madara to manipulate the entire shinobi world into war. Motivated by the death of Rin Nohara, Obito fulfills Madara's revival and Eye of the Moon (Tsuki No Mei) plans. In his own way, Obito cleverly plotted to protect Konoha from the same pain he endured.
Obito’s tactics unleashed the kyuubi who destroyed Konoha (killing Kushina Uzumaki and Minato Namikaze) and convinced Itachi to massacre the Uchiha clan. Before his death, this villain redeemed himself as Obito shared his chakra with Kakashi, allowing him to manifest both Mangekyo Sharingan and help Team 7 to defeat Kaguya.
Kabuto Yakushi
Born into a shinobi-less orphanage without any special techniques or bijuu, Kabuto became a chief strategist infiltrating many villages and inciting some of the series’ biggest arcs, from the Chunin exams to the Fourth Great Ninja War.
In Naruto: Shippuden, Kabuto reanimated essentially every dead character in the franchise to both provide the army for Tobi in the war and force the Akatsuki to comply with his demands. That certainly made him one of the more formidable Naruto: Shippuden villains in a storyline crowded with Akatsuki members. Finally, he was the first living character to discover that Tobi was not actually Madara and one of few to master senjutsu.
Itachi Uchiha
Praised as a genius, Uchiha Itachi was one of the youngest anbu black ops and single-handedly massacred his clan as a teenager. From Sasuke’s vengeance to Kabuto’s izanami, Itachi was a master of deception from day one, and his character arc is a favorite amongst Naruto fans.
Itachi’s brilliance was evident in his manipulation of the sharingan: he implanted the Amaterasu in Sasuke's eyes to kill Tobi (which nearly succeeded) and implanted Shisui's eye in Naruto, which allowed him to reclaim control of his reanimated body and end Kabuto's Edo Tensei technique.
Danzo Shimura
Unlike most of the Naruto villians, who relied on inserting themselves into conflict, Danzo played more political games in Konoha. Danzo founded and led Root, where he cultivated great shinobi such as Itachi, Kakashi, Orochimaru, Kabuto, and Yamato who would play major roles in the series. Simultaneously, he brainwashed many village leaders to pursue his own ideas of peace and power.
Danzo convinced Hiruzen to subject the Uchiha clan to Konoha's police force, which eventually led to their massacre. Then, he stole Shisui Uchiha’s eye to prevent a peaceful end to the attempted Uchiha coup and persuaded Itachi to assassinate the clan allowing Danzo to accumulate sharingan. At the Five Kage summit, Danzo almost bewitched the Five Kage to make himself the Supreme Allied Commander of the ninja world.
Orochimaru
Orochimaru was one of Konohagakure’s legendary Sannin and nearly accomplished his life ambition to learn the world’s secrets. Even as a genin and pupil to Hiruzen, Orochimaru’s intellect was considered to be once in a generation.
After performing countless unethical experiments, Orochimaru discovered numerous forbidden jutsu including Edo Tensei and cursed seal techniques (which he passed to Kabuto) eventually attaining immortality. In the Fourth Great Ninja War, Orochimaru’s summoning of the 5 Hokage was the turning point for the heroes' comeback.
Of all the villains in the Naruto franchise, it is no surprise that Orochimaru was one of few still alive by its conclusion. He's often the best villain in Naruto, but there are a pair more intelligent.
Madara Uchiha
Before this death, Madara launched a master plan to revive himself, capture all of the bijuu, and activate the infinite tsukuyomi. Amazingly, most of his plan occurred over several decades while he was still dead! That's an impressive feat for a Naruto villain.
To accomplish his schemes, Madara deceived Obito into loyalty and placed a cursed tag on Obito's heart to prevent his betrayal. Additionally, Madara planted the rinnegan in Nagato as a fail-safe revival plan and entrusted his plans to Zetsu (admittedly a bad gamble but thorough nonetheless). Finally, Madara bequeathed his name onto Obito and this fear of Madara still being alive became the foundation for the Akatsuki's credibility.
Zetsu
Zetsu was the ultimate undercover agent of the entire series and worked in secrecy for over a thousand years to revive Kaguya while he manipulated almost every major villain along the way.
Black Zetsu tempted Indra to take Asura’s inheritance, which led to the first major shinobi conflict. Later, Zetsu revised the Uchiha clan’s Stone Tablet, which deceived Madara into recreating the rinnegan. Possessing both substitution technique and nature transformation, Black and White Zetsu were incredibly influential to Madara, Obito, and the Akatsuki and provided significant support for the Fourth Great Ninja War. There would be no major Naruto villains without Zetsu's ploys.