Flying Witch follows Makoto Kowata, a young apprentice witch who leaves her parents' home in Yokohama when witchcraft tradition calls for practitioners to become independent at 15. She travels north to Aomori with her black cat familiar, Chito, drawn to a region favored by witches for its rich nature and its closeness to magic. There, she begins a new life with her second cousins, Kei Kuramoto and his little sister Chinatsu, while trying to balance ordinary high school days with the quiet demands of supernatural training.
As Makoto settles in, Flying Witch lingers on the small and strange details that shape her everyday life: an encounter with an anthropomorphic dog fortune teller, the peculiar magic training she receives from her older sister Akane, and the gentle ways witchcraft slips into the routine of friends and family. The series turns that peaceful setting into a slice-of-life story about growing up, finding a place to belong, and discovering how wonder can live alongside the ordinary without ever overwhelming it.