 If you liked
Gakuen Alice
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 ...then you might like
Boku no Hero Academia
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Government-established elite schools for gifted children with super powers.
Perfectly ordinary main characters (reunited with their prodigious childhood friends) without any strenght or specialty - for the first fifteen minutes.
Powerful, genius boys with unapproachable personalities.
Lots of quirky (pun intended) classmates, unique teachers and comedic antics.
Despite being of different demographics, both deal with themes of friendship, bullying, doing good and pursuing goals.
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Recommended by RenaPsychoKiller
Both protagonist has a special power and both enter a school for that special power.
Differences are
- in Boku No hero academia (BNHA) the mc didn't have a power (quirk) until he was given one.
- in Gakuen Alice (GA) the mc didn't know she had a power (alice).
- in BNHA most people have a quirk but in GA only some have an alice.
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Recommended by Rising_Aurora
Gakuen Alice: MC enters school and thinks they have no Alice (powers) but actually has one. Alices are a secret from the public and thus the school is attached to a secret society of Alice users.
BNHA: MC is quirkless (no powers) but he is given one and he uses it to enter his dream school. The majority of the general public have quirks.
Both MCs have their childhood friend who enters the same school but in Mikan's case she wanted to attend the school because her friend Hotaru is there while Deku entered the school at the same time as his childhood friend Bakugo.