Hoernle is perhaps best known for his decipherment of the Bower Manuscript collected by Hamilton Bower in Kucha (Chinese Turkestan). Bower found the birch-bark manuscript in 1890 and it was sent to Hoernle in early 1891. Within months, Hoernle had deciphered and translated it, establishing it to be a medical treatise and the oldest known manuscript from ancient India. His fame led the British India government to seek more manuscripts and archaeological items from Xinjiang (China) and Central Asia, sending him 23 consignments of discoveries before he retired.