Tensei Danshi ~Onna ga Otoko ni Time Leap~

Born female but identifying as male, Shima drifts through school alone, only finding comfort in venting to café owner Runa, a transgender woman who understands him in a way no one else can. Then everything changes. After a tragic accident, Shima awakens in Runa’s body in 1999, back when Runa was still living as a teenage boy. Now in a male body, Shima must face the intense sexual awakening of a boy going through puberty.