Set in August 1975, Boku no Natsuyasumi follows the player character Boku, a city-dwelling nine-year-old boy sent to stay with his extended family in the countryside for a month while his mother prepares to give birth to a second child. The game is framed as the recollection of the now-adult Boku, who occasionally narrates the story.

Boku stays in the home of his paternal aunt Kaoru Sorano, her potter husband Yusaku, and their two daughters: fifteen-year-old Moe and eight-year-old Shirabe. Over the course his month-long vacation, Boku stays in a bedroom peculiarly already decorated with objects typical of a boys' room and maintains a picture diary documenting his various activities and exploits, the precise details of which vary depending on gameplay choices and story events undertaken by the player. One day, the Soranos are visited by a priest and are led in prayer session around the family's shrine; the initially confused Boku learns that Kaoru and Yusaku once had a son who is now deceased, and that Boku is staying in what was his bedroom.

On the penultimate day of Boku's vacation, Shirabe goes missing, and Boku is able to track her to a large sunflower field. Shirabe, who has thus far been distant and irritable towards Boku, opens up to him and tells him that she does not want him to leave. On August 31, Boku's father returns to bring him home; as Boku departs while watching the Sorano family waving goodbye, his adult self narrates that it was a summer he would never forget. The game concludes with an epilogue set twenty-five years later depicting Boku's life as an adult, with multiple possible scenarios contingent on choices made by the player throughout the game.