Why didn't Naruto pass the academy exam when Lee was able to? Lee could not use chakra and thus could not perform any of the 3 techniques. However, Lee managed to pass the academy exam, while Naruto couldn't.

Why did Naruto fail when he could easily perform the Henge and Kawarimi and clearly had too much chakra for the Bunshin?
I believe Rock Lee was an exception, he excelled in Taijutsu to make up for his lack of skill in Ninjutsu and Genjutsu. Naruto on the otherhand initially started off bad at all 3 types of jutsus.

There also doesn't seem to be a formal exam, Iruka and the sensei's make the overall decisions hence why Naruto became a Genin despite failing the "true" exam.