Bretschneider ble legeutdannet ved Universitetet i Dorpat i Dorpat i Estland, og ble først postert som lege ved den russiske legasjon i Teheran. Årene 1866-83 var han så russernes legasjonslege i Beijing.
Hans omfattende vitenskapelige forfatterskap gjaldt dels middelalderens øst- og sentralasiatiske historie og geografi, dels østasiatisk botanikk, særskilt tolkningen av den kinesiske botanikken.
Verker i utvalg
History of European Botanical Discoveries in China, 1898, (Nachdruck: Leipzig, Zentral-Antiquariat der DDR 1962)
Botanicon Sinicum. Notes on Chinese Botany from Native and Western Sources. 3 bind. London, Trübner 1882/1892/1893 (Nyopptrykk av alle bind i Shanghai 1895)
Part 1 Notes on Chinese Botany from Native and Western Sources, 1882
Part 2 The Botany of the Chinese Classics: With Annotations, Appendix and Index, med Ernst Faber, 1892
Part 3 Botanical Investigations into the Materia Medica of the Ancient Chinese, 1895
Mediaeval Researches from Eastern Asiatic Sources: Fragments Towards the Knowledge of the Geography and History of Central and Western Asia from the 13th to the 17th century, London, Trübner's Oriental Series 1888 (2 Bände) (Nachdruck: Frankfurt a.M.: Institute for the Hist. of Arabic-Islamic Science at the J.W. Goethe Universität 1996)
Recherches archéologiques et historiques sur Pékin et ses environs, Paris, Leroux 1879 (Publications de l'école des langues orientales vivantes; Série 1, 12)
History of European Botanical Discoveries in China, London, Sampson Low, Marston 1898, 2 bind (Nachdruck Leipzig, Zentral-Antiquariat 1981)
Map of China and the Surrounding Regions. 2nd edition. Kelly & Walsh, 1900 (Online)
Die Pekinger Ebene und das benachbarte Gebirgsland, Gotha, Perthes 1876 (Petermann's Geographische Mittheilungen. Ergänzungsheft N° 46)
Fu-Sang, or Who Discovered America, Peking 1870
Ta-Ts'in Kuo, S.-A., Peking 1870
Notes on Chinese Medieval Travellers to the West, Shanghai 1875
Notices of the Medieval Geography and History of Central and Western Asia, London 1876
Early European Researches into the Flora of China, Shanghai: American Presbyterian Mission Press 1881
On the Knowledge Possessed by the Ancient Chinese on the Arabs, London 1871
Litteratur
Vitaly Naumkin (utg.9. The Bretschneider Albums. 19th Century Paintings of Life in China. Reading, Eng. Garnet 1995; ISBN 1859640109 (Catalogue of the Remarkable Paintings commissioned in 1866 by Emil Vasilyevich Bretschneider)
(nekrolog) «Dr. Emil Bretschneider»; i: The Geographical Journal 18, No. 1 (Jul., 1901), s. 95