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Wielding a Genjutsu in the world of Naruto meant total control over an individual's opposing force. This unique skill falls under the category of Ying release, otherwise known as nature-transformation, and controls the imagination of any individual, be it a human or a different species.
While Genjutsu was one of the core aspects of the power showcase in the main series, it also defined the ability of the one wielding it. The whole point of the show was to stop the bad guys from casting a massive Genjutsu on the entire world and enslaving the whole of humanity.
However, with such a powerful ability being shown throughout the series, some things remained unanswered for fans and viewers. Since the absolute power of Genjutsu relies so much on Chakra on both sides, many wonder if the ability will entirely work on someone with Chakra in them. The short answer is: yes.
Genjutsu in Naruto can work on someone without Chakra
To understand how Genjutsu works on non-Chakra users, one must understand how the ability functions. Let us track back to when Jiraiya gave a small lesson on Genjutsu to Naruto. He said the following:
"To control the Chakra flowing through and linking their cranial nerves. It is a jutsu requiring quite a high level of Intellect. Genjutsu is something that works on your opponents' five senses."
A strong Genjutsu will always be more potent while affecting the senses of controlling the Chakra flow rather than controlling the Chakra itself. Hence, the main point of using the ability on an opponent was never about Chakra but senses. Certain Genjutsus also have the ability to fill Chakra as a medium and affect the nervous system.
The Infinite Tsukuyomi is a prime example of Genjutsu's ability against non-Chakra users. It is known to be the strongest Genjutsu in the Naruto series, which can enslave everyone, be it Chakra-wielding Shinobis or just regular human civilians with any Chakra flow.
This was demonstrated by Kaguya Otsutsuki and Madara Uchiha when both used their Rinne Sharingan to cast the spell by reflecting it off the Moon. Since Infinite Tsukuyomi is considered a Genjutsu, then it can be safely deduced that the ability can work on every being alive on the planet, regardless of their Chakra.
Apart from this, the simple ocular Genjutsu of both Itachi and Shisui doesn't require Chakra on the opposing party as well. The one casting Genjutsu can fill the victim's nervous system with Chakra and manipulate it in regular ways.
The only people that could be immune to this are the ones who could sense Genjutsu or the ones who could block Chakras. Then again, to have a decent grasp of the Chakra system, a person must undergo rigorous training, something that ordinary civilians in Naruto aren't accustomed to.
