The dense inflorescence of Habenaria lithophila is many-flowered, bearing from 10 to 30 flowers. The erect bracts growing from below each flower become from 1 cm to 2 cm long. Flower pedicels, at least 1 cm long, are topped by curved, ridged ovaries.
The flowers of H. lithophila are fragrant in the evenings. At least some of their pollinators are moths. Flowering happens from late spring to mid-autumn (Liltved and Johnson, 2012; Pooley, 1998).