Saki Miyanaga, a high school first-year student, does not like mahjong because her family would always force her to play it and punish her regardless of the outcome of the game. Due to this, she learned how to keep her score at zero, neither winning nor losing, a skill said to be more difficult than actually consistently winning. However, her friend from middle school, completely unaware of such circumstances, convinces her to visit the school's small mahjong club upon entering into high school. After the club discovers her ability, they recruit her permanently and convince her to win instead of breaking even. She easily does so with her skill and discovers a new love for mahjong, along with a friendship with her fellow club member, Nodoka Haramura. This leads the team to enter the prefecture's high school mahjong tournament with the goal of reaching the national high school competition.

The side-story manga, Saki: Achiga-hen episode of Side-A, is based in the area around Yoshino, Nara and follows a girl named Shizuno Takakamo, an old friend of Nodoka's, who used to be in Achiga Girls Academy's mahjong club together. A few years after the club disbanded and the two split up, Shizuno spots Nodoka on television as she makes her stride in mahjong. Wanting to see her old friend again, Shizuno decides to revive the Achiga Mahjong Club so that she can face against Nodoka in the inter-high national championships. The spin-off, Shinohayu the dawn of age, shows the childhood of the various pro mahjong players in the series, focusing on a girl named Shino Shiratsuki who enters the world of competitive mahjong to seek out her mother who disappeared one day.