The story takes place in a world where historical World War II–era tanks are maintained for sport-style warfare competitions and large carrier ships, known as Academy Ships, support mobile sea communities. Of the many activities high school students can participate in, one of the most popular is "sensha-dō" (戦車道, lit. "the way of the tank"), the art of operating tanks, which is considered a traditional martial art for females.
Miho Nishizumi, a girl from a prestigious family of sensha-dō practitioners who became traumatized by a past event, transfers to Ōarai Girls High School to get away from sensha-dō, as she presumed the school was no longer practicing the sport. However, shortly after Miho begins her new school life and makes some new friends, the student council announces the revival of sensha-dō at Ōarai and coerces Miho, the only student with prior experience, to join. While reluctant to join at first, having practically been forced, Miho soon warms up to sensha-dō and they enter a national championship, facing off against various other schools, in a competition that becomes a serious matter after Miho and the others learn that their school will be closed should they not win.
The spin-off manga, Girls und Panzer: Little Army, follows Miho in her elementary school days as she participates in sensha-dō alongside her friends Emi, Hitomi, and Chihiro.