Who are the top 3 smartest characters of the series

[Sagebee]

And in order also this doesnt count strategic or battle intelligence but strictly academic

 

[Kakooli]

1. Sakura
2. Inner Sakura
3. Tsunade/Kabuto

 

[Aadhishrm1]

1.Minato
2.Itachi
3.Orochimaru

 

[Imp]

Black Zetsu, Madara and Oro.​

 

[salamander uchiha]

Since they didn't have academies in the time of Lord Madara I'll leave them out.

Itachi
Sakura/Shikamaru.

 

[Ninetailsfox00x1]

Shikamaru daddy, shikamaru and Itachi

 

[Michelle]

Shikamaru
Itachi
Orochimaru

 

[Melanin]

Black Zetsu
Itachi
SO6P

Noteable mentions:

Madara
Minato
Sasuke
Hurizen
Orochimaru
Shiakmaru
Tsunade

 

[Eos]

Shikamaru
Orochimaru
Itachi

No specific order.

 

[Azarath Metrion Zinthos]

Minato and Itachi are definite for their positions since they're said to be one and two respectively. Third place would most likely be Sakura since at one point she mentioned of having "always" scored 100% on tests.

 

[Tyris]

Itachi.

Oro

Tobirama/Minato

 

[ErickJh0n]

Itachi
Shikamaru
Orochimaru

 

[Ldude]

The following characters are given as having 5/5 intelligence in Databooks 1-3: Chiyo, Hiruzen, Itachi, Kabuto, Kakashi (he has 4.5 in the 1st databook and is upgraded to 5 for the 2nd and 3rd editions), Orochimaru, Sasori, Shikamaru, and Tsunade. As per the original question which differentiates between strategic and academic intelligence, there is a good deal of overlap because the knowledge ninjas tend to accumulate is that which will help them in battle or medical knowledge. Another issue with only looking at those deemed most intelligent is that the definition of intelligence used seems to be different for each character. At times it is used to refer to their genius as children; for some it is used to explain years of study; for a third class yet, it could mean those who commit to running experiments and create their own jutsu. Distinction between fluid and crystallized intelligence is rarely given. I'll summarize what we know about high-intelligence characters to further differentiate them:

Chiyo
Died at age 73. From the Third Databook: "Long ago, the young kunoichi Chiyo amazed shinobi from foreign lands with her extraordinary skill in medical ninjutsu, taijutsu, and puppet jutsu." Developed Kishotensei (self-destruct) technique. Served as advisor to Suna after she retired. Quote: "True alliances are nothing more than pipe dreams."
Hiruzen
Died at age 69. From the First Databook: "Aside from “Professor”, the Third Hokage has been called “the most powerful of all time” and “genius”. Unfortunately, he could not find a fitting successor to pass on his knowledge and techniques." Quote: "YOLO."
Itachi
Graduated Ninja Academy at age 7, promoted to Chuunin at age 10. Died at age 21. From Third Databook: “Because he was naturally gifted, he was chosen to become a spy. His sharp intelligence allowed him to give even the most minute detail perspective…Itachi joined the Akatsuki, which posed a threat to Konoha, so that he could keep an eye on its movements from the inside.” Possesses knowledge of legendary items.
Quote: “Every single one of us goes through life depending on and bound by our individual knowledge and awareness. And we call it reality.”
Kabuto
Graduated Ninja Academy at age 10. From the Second Databook: "Very good at understanding the situation and analyzing data. Choices made through these skills are without flaw. An ability that is shoulder to shoulder to his medical skill is reading people’s minds. Through expressions and words and actions, he can accurately pierce through the psyche."
Quote: "If I don't always have at least one of each age range stored in chronological order in my scroll, I get... anxious."
A reminder for those who underestimate Kabuto:

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Kakashi
Graduated Ninja Academy at age 5, promoted to Chuunin at age 6. He is one of the few characters who reads as a hobby, however these books tend to be "romance" novels. Intelligence is rooted in battle strategy. Quote: "I'm just a piece of trash…"
Orochimaru
Graduated Ninja Academy at age 6. Legendary Sannin. His extensive research on atypical ninja abilities is unrivaled by any other character in Naruto. The Third Hokage said [of Orochimaru]: "All of my knowledge is still no match for his talent." Possesses knowledge of legendary items and rare jutsu. Founded his own village so he could run illicit experiments on people with reproducible results, e.g. he was Juugo's curse power in multiple subjects, Senju wood release in himself, and cloning. Quote: "I want to obtain all the techniques and gain a true understanding of everything in this world."
Sasori
Graduated Ninja Academy at age 7, promoted to Chuunin at age 8. Died at age 35. Vast knowledge of poisons, puppetry, and the human body. Quote: "I even had to use my last trick..."
Shikamaru
Graduated Ninja Academy at age 12, promoted to Chuunin at age 12. From the Second Databook: "Even in individual battles, Shikamaru’s brain acts as a great weapon. However, it is in team battles that Shikamaru can exert his full ingenuity. When Shikamaru commands a shinobi team all of different characteristics and aptitudes, then his abilities and potential will become unlimited!!" From the Third Databook: "It is said that Shikamaru has an IQ that exceeds 200." (Note: One could expect someone with an IQ of 200 to appear once for every 76 billion people.) Masashi Kishimoto, answering who he would want as a boyfriend: "Shikamaru because he's intelligent and I think he'd succeed in life."
Tsunade
Graduated Ninja Academy at age 6. Legendary Sannin. Known as the greatest living medical ninjutsu user, rivaling Chiyo. Quote: "Although I am a descendant of the First Hokage, it's true that I don't know how to use Wood Release. And compared to him, who was able to use medical ninjutsu without even making seals, it's true that my own ninjutsu is nothing to brag about."

It should be noted that the age of promotion to different ranks is not a good indicator of intelligence. Ninja in times of war were pushed to go through the motions sooner than they otherwise would have due to short supply. They are given to compare within-generations but are virtually meaningless between-generations. Some of the above died too young to accumulate the same level of knowledge as the others. Some were only ranked as highly intelligent because of their renown for battle strategy. Because the original question asked about academic intelligence, bias was given towards those who were older, known to dedicate time to study, and known for academic achievement. All things considered, here is how I would rank the above:

1. Orochimaru
2. Hiruzen
3. Kabuto
4. Chiyo
5. Tsunade
6. Sasori
7. Itachi
8. Kakashi
9. Shikamaru

There are others in Naruto who have been overlooked due to their lack of battle prowess. Nonetheless, they possess unique intelligence unforeseen in their respective fields. A moment for the fallen:
Teuchi "The Ramen Guy"
Cat Granny
Great Toad Sage

 

[ETHx]

Kabuto
Itachi

Those two seem to be the ones with the highest academic prowess.

 

[To Whatever]

Katasuki and Akita are on the bleeding edge when it comes to advancements in ninja tools and overall inventions.

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Orochimaru has successfully figured out how to clone people and solved the human genome to the point where gene splicing and creating synthetic humans with KKG is possible.

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In terms of Ninjutsu. Hagoromo so far is the pinnacle of it all assuming he was the first to use Creation Of All Things and the Super Seal used against Kaguya.

 

[Imp]

Shikamaru daddy, shikamaru and Itachi

Shikamaru and his dad I would say were smart battle-wise. I wouldn't put them near Itachi though; he beleaguered most of his contemporaries.​