Hoya thomsonii was formally described by Joseph Dalton Hooker (1817–1911), a highly influential British botanist and explorer.
He published its description in 1883 in his monumental work, "Flora of British India."
The species was named in honor of Thomas Thomson (1817–1878), a British botanist and explorer who collaborated with Hooker on many botanical expeditions in India. Thomson collected the type specimen of this Hoya along with Hooker in the Khasia mountains.