I might have it in my strong female protagonist list
Rather than "ninja", this one is about "samurai", but it's basically what you described. http://www.mangago.me/read-manga/samurai_high_school/
It's that one! (๑•ㅂ•)و✧
sorry i was a bit excitedヾ(☆▽☆)
Ahaha no worries. I just wanted to make sure it was the right one and I wasn't misleading you lol
ive been really wanting to read this manga but i cant remember the name it was two twins one a boy the other a girl were both going to a ninja school and they had seperate sections for the girls and guys and they switched places to get into the school the girl wanted to become president or something but couldnt because she is a girl
thankx (⌒▽⌒)