GIKEI: The Genpei War Chronicles

Kanou Yoshitsune is the son of the family that runs Kanou Shrine, a shrine with ties to the Genji (Minamoto) clan. He has a younger sister named Rouko, and his childhood friend Shizuka is the daughter of the family that runs Western Kanou Shrine, situated on the opposite shore.

One day, the three go on a school trip to Kyoto, when Rouko mysteriously disappears at Kuramadera temple. Yoshitsune and Shizuka head to Kuramadera to search for her, but when they reach the temple's main hall, they lose consciousness.

When they open their eyes, they find themselves at the same Kuramadera, yet... something is different. Though in the same location, they are approximately 850 years in the past, in the Heian period.

[From NookGaming]