This species is characterized by its rather slender habit, appressed to spreading pubescence, thin-textured petiolate leaves, inflorescences with the flowers shortly pedicellate and closely set along the primary axis, small white corollas with the tube 2-3 mm long, and small fruits ca. 2.5 mm in diameter.

Gonzalagunia brachyantha is similar to Gonzalagunia rudis in its small flowers and slender habit, but Gonzalagunia rudis has longer calyx limbs and the flowers separated along the inflorescence axis. Gonzalagunia brachyantha is also similar to Gonzalagunia microsepala, which has dense hirsute to villous pubescence.