The flowers of Gymnosporia emarginata are grouped in short axillary or terminal cymes. The peduncle is reduced.
The flowers are 5-merous.
The calyx is composed of a 5 mm long tube and 5 mm long lobes. The calyx is light green yellowish-coloured and glabrous.
The corolla is composed of 5 white-coloured and glabrous petals. The petals are ovate and 3-4 mm long and 2-3 mm wide.
The androecium is composed of 5 stamens with 2-3 mm long filaments and small and ovoid anthers.
The style is short with 3 stigmas.
The ovary is 3-celled with 2 ovules per cell.
The flowers are fragrant.