Sayuri-san no Imouto wa Tenshi follows the story of the Kobayashi siblings, Sayuri and her little sister Mikoto. Due to a divorce they were separated 13 years prior to the beginning of the story. One day Mikoto suddenly appears near Sayuri's workplace, a flower shop, with wings on her back and a halo above her head. According to Mikoto these angelic features were granted to her by god when she asked him to let her see Sayuri. She then begins living in Sayuri's apartment.