The flowers of Pterocarpus santalinus are in simple or few-branched, axilllary or terminal racemes. The pedicel is about 1 cm long.
The calyx is 5-6 mm long and 3-4 mm across with 5 small and triangular lobes. The calyx is light green and tomentose.
The corolla is composed of 1 ovate-globose, 1x1 cm and clawed standard, 2 clawed and 7x5 mm wings and 2 clawed, 5x3 mm conate keels. The petals are yellow and glabrous.
The androecium is composed of 6 stamens. The filaments are 5-6 mm long with ovoid anthers.
The pistil is composed of slender and 3-4 mm long style and a trifid stigma. The ovary is stipitate and 4-5 mm long.
The flowers are fragrant.