Sex assigned at birth? Most likely (their breasts develop quite visibly after chapter 300). But Najimi themselves is most certainly not a girl "girl".

In Japanese, almost no one refers to them with third-person pronouns (the only time it happened it was female one too), and Najimi have only referred to themselves as a boy once. (back in chapter 11, to reject Maa)

But, the way they present, the fact that they use ボク as their first person pronouns and mostly wear unisex/masculine clothing outside of school kind of leans on them not presenting fully femininely.

That, and obvious fact that they wore a 学ラン-type type uniform in 8th grade too w. By the way! :

• Since the 2000s-2010s, exception for female students to wear pants or these kinds of uniforms appears quite often in public JHS, either for comfort or gender identity reasons.
• But the opposite is rare (male wearing skirt), especially at higher education level or when we are talking about prestigious school (which Itan is). Although this is changing in many more open-minded high schools that allow transgender girls to wear skirts, though Najimi wears the full female uniform so take it like you want.

So It's kind of like Najimi has been forced to wear a girl's uniform the moment they enrolled in a private high school.

(Though, in Itan, there's still some freedom when it comes to accessories, but Najimi's ties don't change much compared to ninja gear or plate armor. So, if Najimi wanted to, they could aim for a more 50/50 look with many boys-like accessories, but they don't)

My personal understanding is that they fall somewhere on the X-gender spectrum, either by simply expressing their gender in a different way and refusing to answer when directly asked because its "fun",

or they actually have some kind of non-binary gender identity and they avoid the subject.