Even within the famed and battle-adept Uchiha clan, Itachi was a genius of such talent, he consistently showed prowess well-beyond his years, effortlessly learning new jutsu from simple observation, and rising rapidly through the ninja ranks. His prowess rivalled Shisui Uchiha, who was well-regarded as the strongest Uchiha of their time. He was highly proficient in all three main ninja skill sets and gained praise from allies and foes alike; Orochimaru, one of the Sannin, openly admitted Itachi was stronger than he was. Obito revealed that despite being weakened from illness and Sasuke having absorbed Orochimaru's power, Itachi could have killed Sasuke during their battle if he wanted to. Even when restraining himself, a team of jōnin were still pushed to their limits against Itachi.

As an Uchiha, Itachi's chakra was naturally strong, it is unknown how his actual reserves were affected by his terminal illness. Just three uses of his Mangekyō Sharingan in a single day made him unable to use his Sharingan and he would require significant rest afterwards to regain his strength. This also prevented him from participating in prolonged battles. Itachi had very refined chakra control, however, which compensated for this, even able to perform his techniques with one-handed seals.
Although not his preferred method of combat, Itachi was very skilled with taijutsu – enough to easily defeat three members of the Konoha Military Police Force at the age of eleven. He had exceptional speed and reflexes, able to compete with Shisui, who was well-famed for his own speed. His quickness was particularly noted with his hand movements, able to make hand seals too fast to be perceived normally; even skilled Sharingan-users had difficulty following him. His speed could move great distances in an instant as if by displacing himself, giving his opponent little chance to react or initiate a counter-attack. Itachi also showed remarkable fortitude. Despite spending years afflicted with a crippling disease, he was able to maintain his composure at all times and still battle at near-perfect form. Itachi set the record for completing the Forest of Death in his Chūnin Exams while still 9 years old, at 5 hours and 37 minutes, while taking the exams solo. He could use chakra to enhance his strikes.

Itachi could summon crows, which he would typically call forth in flocks to swarm opponents and distract them. He even integrated crows into clones of himself that would draw opponents' attacks. He was likewise able to create shadow clones and from which could lure in opponents before exploding. Itachi was also well-versed in fūinjutsu, particularly those that would activate in the presence of a specific person's Sharingan. From his time in Anbu, Itachi became proficient in stealth, infiltration, and assassination.

Itachi's nature transformations included Fire, Water, Wind, Yin, and Yang Release. As an Uchiha, he had a natural affinity for Fire Release, mastering the clan's Great Fireball Technique at a very young age. He would often coat shuriken with fire to increase their offensive capacities. With Water Release, Itachi could perform the Water Dragon Bullet Technique without an external water source, as well as shape existing water into tendrils to strike his opponents from all directions.

Consistent with his pacifist nature, Itachi specialised in genjutsu, where the illusions would typically involve crows. Regarded as one of Konohagakure's best users, even without the aid of his Sharingan, his illusions have remarkable potency, able to seamlessly affect his targets without them realising it, while on guard, and also perform them by merely pointing at his target. He is noted by Ao to have such high prowess that he could use genjutsu to control other individuals outside the range of even the Sensor Division. Itachi could also use genjutsu to share information or psychologically disable opponents, letting him end the fight instantly.

Itachi awakened the Sharingan at age eight, after witnessing his team-mate Tenma Izumo's death, and soon after mastered it. From a young age, he demonstrated skill and power superior to most members of his clan. In the anime, his prowess and exploits with it earned him great fame as "Itachi of the Sharingan" (写輪眼のイタチ, Sharingan no Itachi). He tends to keep his Sharingan active near-constantly with minimal drain on his chakra levels. The Sharingan allows Itachi to see the flow of chakra, predict movements, as well as facilitate his use of genjutsu. Against other genjutsu users, he could turn their genjutsu against them. Also, with the Sharingan he could perform Izanami, a counterpart to the more dangerous Izanagi.

Itachi awakened the Mangekyō Sharingan after witnessing Shisui's suicide. Its design was three spiralling curves around the pupil. With both eyes, he could use Tsukuyomi, a genjutsu that trapped opponents' minds in an illusory world, altering their perception of time. With his right eye he could use Amaterasu, igniting whatever he looked at with black flames that would burn anything, including fire itself. He had the ability to extinguish Amaterasu.

Having awakened the Mangekyō in both his eyes, Itachi could also use Susanoo. With its simplest manifestations, he could produce extra arms or bones to improve his options in a fight. When used in full, Itachi was surrounded by a spectral warrior that would protect him from damage. In addition to the chakra swords and Yasaka Magatama common to all Susanoo, Itachi's Susanoo wielded the Sword of Totsuka – an ethereal sword with the ability to seal any person it pierced into its gourd—hilt – and the Yata Mirror – a shield that was said to reflect any attack by changing its chakra nature to counterbalance an attack. The simultaneous use of both weapons made Itachi's Susanoo essentially invincible. Using any of these techniques required large amounts of chakra. If he used these techniques too often in a short span of time, Itachi would become so fatigued that he would deactivate his Sharingan altogether. Every time he used his Mangekyō Sharingan his eyesight deteriorated, a process that would progressively worsen on each occasion. Early uses of the Mangekyō would only cause his eyes to bleed, but by the end of his life he reached the point where he was nearly blind, most things looking to him like mere blurs. He does not suffer these shortcomings after his reincarnation and can use all his Mangekyō techniques without problems.

Itachi was a highly intelligent individual, having the second highest scores in the history of the Chūnin Exams written test behind Minato Namikaze. Composed and observant; he thought very quickly and remained calm in a fight, enabling him to respond with maximum efficiency and with the smallest likelihood of misjudging circumstances. Even at a young age, he was always calculating and methodical in his approach to the situation at hand, leaving little room for error. He took several precautions for Sasuke and against Tobi that he planned would activate after his death. Even Tobi admitted if he didn't keep some secrets from Itachi, he would have been killed by Itachi's trap. During his infiltration of Konoha, Itachi was also able to subtly leak Akatsuki's goals to Kakashi, Kurenai, Asuma, and Jiraiya without arousing Kisame's suspicions.