Cyrtandra wagneri is a shrub or treelet that reaches up to 3 meters in height, with a central stem that is solitary or sparsely branched, measuring up to 2.5 cm in diameter. Its parts are covered with golden-to-dark brown villosulous-hirtellous hairs that are 0.4–0.9 mm long and either spreading or antrorsely curved. The leafy stems are about 5–10 mm in diameter, with internodes spanning 2–3 cm. The leaves are simple and opposite, with elliptic to oblong-elliptic blades measuring 20–41 cm long and 8–18.5 cm wide. The leaves of a pair can be equal or subequal and either symmetrical or somewhat asymmetrical, with densely strigillose-hirtellous upper surfaces and moderately to densely velutinous-hirtellous lower surfaces, featuring crinkled hairs that are denser along the veins and margin. The flowers occur in cauliflorous inflorescences near ground level or up to 2 meters above, initially erect but becoming pendulous with age. These inflorescences are dichasial, measuring 4–6 cm by 4–9 cm, and comprise 2- to 3-branched cymes with 12 to 25 flowers. The calyx is actinomorphic (radially symmetric), green when fresh, and 13–15 mm long, with lobes lanceolate to linear-oblong, densely golden brown strigulose-hirtellous on the outside and strigulose inside. The bilabiate corolla is white, with a subcylindrical tube that flares slightly at the mouth and is (12)15–22 mm long. It has five stamens, with the upper two being fertile and the others staminodial. The superior ovary is ovoid, 5 mm long, and has two carpels with parietal placentation. The fruit is a white, fleshy, or firm berry, ovoid to ovoid-ellipsoid, measuring 13–16 mm by 7–8 mm, often with a persistent stylar beak. It produces numerous pale brown, ellipsoid seeds, each approximately 0.3 mm long with a reticulate surface. It is restricted to steep slopes (up to approximately 45 degrees) of stream banks, where it roots in rocky brown clay soil. It typically grows under moderate to dense shade in wet forests between 823–869 meters.