I thought there was no girl baseball in high-school because there's no tournament for them in Japan anyway, so it's a waste of time. Finding another team is probably nearly impossible.
But hey, it's manga world.
There are Japanese schools with female baseball clubs. They do have tournaments.
ONE tournament. For all Japan... a bit of research yielded this :
"in Japanese high schools, female teams are rare and usually only exist in private schools, who compete at the National High School Women’s Baseball Championship in Hyogo Prefecture every August. Girls with an interest in the sport who attend public schools often resort to joining their male baseball team at school in the position of managers or assistants."
Though in my research, I stumbled upon the single ever female pitcher to have played professionally in male teams, Eri Yoshida.