H. japonicum is unusually small for a St. John's wort, growing only 2–5 cm (0.8–2.0 in) tall.

[5] Its stems are green and 4-angled, with 2–52 mm (0.1–2.0 in) long internodes that usually exceed the leaves.

[6] The flowers are 4–8 mm (0.16–0.31 in) in diameter and their petals are bright yellow or orange.

[7] The seeds of H. japonicum closely resemble those of the extinct paleospecies Hypericum tertiaerum.

[8] The species is found across the Indian subcontinent, China, Southeast Asia, and Oceania.