About seven months after Naruto's sixth birthday, the Old Man allowed him to enter the Shinobi Academy. Based on one of his momma's stories, he loudly proclaimed that he would be Hokage when he grew up. The class laughed at him and the teacher got angry.
The Academy was boring. Mostly it was learning history, math, and language with some pretty simple physical exercises thrown in. His momma told him the curriculum would expand as he got older.
His teacher at the Academy treated him worse than the orphanage matrons. His work was graded much more harshly than anyone else's. By this time his handwriting was impeccable, but the teacher always found mistakes. When he asked his momma about it, she explained that she had taught him the Uzu style which was slightly different than the Hi style, but that the instructor should not be marking him down for that difference. The few times he tried adding the extra flourishes of the Hi style, the instructor still found excuses to mark him down, so he went back to the Uzu style.
Besides grading his work more harshly, the teacher also ignored him. If he raised his hand or stood up, the instructor "didn't see him." If he just spoke his question, he was sent into the hall for "disrupting the class." Sometimes he was sent into the hall without doing anything. Despite this, he was in solidly in the middle of the class. He shuddered to think of where he would be if it were not for his momma helping him. He thought about complaining about the unfair treatment to the Old Man, but decided that whining about only getting average scores was not his style and he started pranking the teacher instead.
His momma confessed that she had been a prankster when she had been in the Academy, which only made him redouble his efforts. At first, he got caught pretty often, which dropped his standing to near the bottom as the teacher took away "citizenship points." After a while he stopped getting caught, but since he had a reputation and was disliked, the teacher always blamed him anyway.
The other students treated him like the orphans did, except that the teachers did not stop the bullying. He made a few friends at first, but they did not last long. One or two admitted that their parents had told them to stay away from him. Before long, even the ones that had not been warned by parents, stayed away due to peer pressure. The bullying led to fights that were always Naruto's fault no matter who started it, which contributed to his loss of "citizenship points." Naruto's taijutsu was good enough that he usually won, which limited the physical bullying.
He did make an effort to stamp out bullying whenever he encountered it. Usually his efforts went unrewarded. Sometimes he would make a friend for a few days, but inevitably they would succumb to the peer pressure or their parents' wishes.
The most notable people he helped were a pink-haired girl who he sometimes saw around the Academy and a pale-eyed girl named Hinata who was whisked away by a servant or relative. The pink-haired girl, Sakura, was friendly for longer than normal, but she succumbed eventually. He saw the pale-eyed girl sometimes, but she never approached him.
In the second Academy year they started basic taijutsu and shuriken practice. Naruto was better than most of the class in both of those due to instruction from his momma, but the instructor usually found a reason to mark him lower than he should have.
He did notice that there were some new kids that got moved in from a different class. The only one that stood out was Uchiha Sasuke. Sasuke was the only kid that routinely beat Naruto in taijutsu. Sasuke's main advantage was that he used a more advanced taijutsu style. He was a little bit aloof, but friendly in general. Sasuke was the only kid that did not ignore Naruto.
He asked his momma if their clan had an advanced taijutsu style. She told them that there had been several but that she only knew one of them.
When he asked to learn it, she said, "The taijutsu style I know is for women. It wouldn't help you that much, Sweetie."
"Why not?" he asked.
"Women's strength comes from their hips, while men's come from their shoulders. Chakra helps offset this, but chakra multiplies the existing strength. A woman will always get more out of a taijutsu style centered around hip movement. A man can use that type of style, but would get more out of one designed around their upper body."
"So I could use your style, it just wouldn't be the best style for me?" he asked.
"Well," she said, "some modifications would still need to be made. At your age there isn't a huge difference between boys and girls, but starting in a few years there starts to be more differences. These are centered around the fact that a woman's pelvis is shaped differently than a man's. Women walk, run, and kick differently. Women also tend to be shorter and a few other things."
"Couldn't you change it to work for me?" he pleaded.
"Maybe, but it would be better for you to pick one that's more suited to you to begin with. It's too bad, because taijutsu was one of my specialties, but I never learned more than the general basics and my specific style."
A few months into the year, Sasuke changed. He was gone from class for a month and when he came back he was not just aloof, but dark and brooding. From that point, Sasuke started ignoring him and everyone else. Naruto heard rumors that Sasuke's clan had been murdered. He tried to befriend the boy, but was brushed off.
When he talked to his momma about it, she took it badly.
"Uchiha Mikoto was my best friend," she said. "Itachi-chan did it!? He was such a nice boy! It's too bad Sasuke is so unfriendly. Mikoto and I always wanted you two to be friends. I'm kind of surprised she hasn't been active in your life."
"I've never seen her," Naruto said.
"Ah, probably politics or her jerk-of-a-husband is keeping her away."
On Naruto's eighth birthday, his momma told him that his daddy was the Fourth Hokage. That made him super excited, since the Fourth was his hero. The pictures in the mindscape house stopped having fuzzy faces. His momma emphasized the importance of keeping the secret since there were many in Iwa and Kumo that hated his daddy and would take the opportunity to take revenge through him. She told him there were even a few in Konoha who did not like his daddy, but he found it hard to believe since his daddy had saved Konoha several times. This made him even more determined to be the best Hokage ever.
In the third Academy year, they learned kunai throwing and more taijutsu.
In the fourth year they awakened their chakra, if they had not already, and learned leaf sticking. If Naruao had not already done so, it would have been difficult as the teacher always sent him out during the explanations on the chakra control exercise and why it was important.
In the fifth year they started to learn their first ninjutsu, the Clone Technique. Despite having good chakra control, Naruto could not do it.
When he asked his momma about it, she said, "Although it's classed as a ninjutsu, the Clone Technique is actually a genjutsu. Uzumaki typically have trouble with genjutsu due to our dense chakra and high chakra reserves, especially genjutsu with small chakra requirements. I could never do the Clone Technique unless I made at least 20 clones."
"Should I do that? Make a bunch of clones?" he asked.
"I would not recommend it," she said. "From what you've told me of your teacher, he would just keep failing you until you could make just one and would look for more ways to sabotage you. I think this will actually be a good test as to whether your teacher actually cares about you. If your teacher actually helps you figure out why you can't do the Clone Technique, he's a good teacher."
"I already know my teacher hates me!" Naruto said. "I don't see him changing his mind."
"Eventually you'll get a new teacher once enough kids drop out and they merge classes."
His chakra reserves kept expanding. This did not help make Clone any easier. To counter that, his momma taught him how to climb trees with chakra.
In the latter part of the fifth year, the class learned the Disguise Technique. The teacher tried to stop Naruto from learning the new ninjutsu because he had not learned the Clone Technique yet. He was able to figure out how to do it by spying on the other kids. He picked up the technique without too much difficulty. He was a little surprised at how easy it was since he thought it might really be a genjutsu too.
"Disguise was easy for me too," his momma admitted. "Much easier than I thought it would be since Clone always gave me trouble. They're actually somewhat similar techniques, although Disguise takes more chakra."
Naruto practiced Disguise extensively, since it was the only ninjutsu he knew. The amount of chakra it took depended on the complexity of the change. Since he had more chakra than his classmates, he did not have any problem changing into almost anything. If he changed his size there was a chakra cost to keeping the technique going, but if it was something his own size, it cost nothing—or almost nothing—to maintain.
His momma also started teaching him the basics of sealing theory. This included the characters used in seals and how the geometry of the seal influenced how the characters related to each other. She had him make some basic seals that changed color when chakra was added to specific characters.
Author's Note: There can be some debate about whether the standard Transformation Technique (Henge) is a real or illusionary technique in canon Naruto. As far as I know only when Naruto is involved can it be shown to be physical, although no one is surprised when he changes into a shuriken that works. My view is that it would be too OP for an E-rank if it were a real, physical change. This is why I call it Disguise in my fics.