Complex sentence: One of Fujimoto's examples is that the girls get higher grades than the boys in the Ninja Academy, but when they all graduate, and the boys on the teams take their "shinobi" career seriously, the girls are unable to keep up with them.
Split into simpler sentences: One of Fujimoto's examples is the girls get higher grades than the boys in the Ninja Academy. When they all become actual ninja, and the boys on the teams they are assigned to take their "shinobi" career seriously, the girls are unable to keep up with them.