Draper wrote a number of books and articles for magazines and journals ([https://scholar.google.com/citations?hl=en&pli=1&user=YcnAATAAAAAJ Google Scholar]). His books include: 
* [https://archive.org/details/elementschemist02drapgoog Elements of Chemistry, Including the Most Recent Discoveries and Applications of the Science to Medicine and Pharmacy, and to the Arts.] by Robert Kane and John William Draper. New York: Harper and Brothers, 1842.
* [https://archive.org/details/bub_gb_IoAR-SpiFGQC  History of the American Civil War.] New York: Harper & Brothers, 1867–70.
* [https://www.gutenberg.org/ebooks/1185 History of the Conflict Between Religion and Science.] New York: D. Appleton, 1874.
* [http://www.h-net.org/~bahai/diglib/books/A-E/D/draper/draptoc.htm History of the Intellectual Development of Europe.] New York: Harper & Brothers, 1863, [https://archive.org/details/historyintellec00drapgoog 1900 edition, v.1],[https://archive.org/details/historyintellec03drapgoog v.2]
* Human Physiology, Statistical and Dynamical; or, the Conditions and Course of the Life of Man. New York: Harper & Brothers, 1856.
* Life of Franklin, Edited by Ronald S. Wilkinson. Washington, D.C.: Library of Congress: U.S. Government Printing Office, 1977.
* Draper, John William. (1875). History of the Conflict between Religion and Science. Henry S. King & Co (reissued by Cambridge University Press, 2009; )
* [https://archive.org/details/scienceinameric00drapgoog Science in America: Inaugural address of Dr. John W. Draper, as president of the American Chemical Society] New York: J.F. Trow & Son, Printers, 1876.
* [https://archive.org/details/scientificmemoi00drapgoog Scientific Memoirs; Being Experimental Contributions to a Knowledge of Radiant Energy.] New York: Harper & Brothers, 1878.
* Text-Book on Chemistry. For the Use of Schools and Colleges. New York: Harper & Brothers, 1851, [https://archive.org/details/atextbookonchem03drapgoog 1861 edition]
* [https://archive.org/details/bub_gb_GgQ5AAAAMAAJ  Text-Book on Natural Philosophy.] New York: Harper & Brothers, 1847.
* [https://archive.org/details/thoughtsonfutur00drapgoog Thoughts on the Future Civil Policy of America.] 3rd ed. New York: Harper & Brothers, 1867.
* Treatise on the Forces Which Produce the Organization of Plants. With an Appendix Containing Several Memoirs on Capillary Attraction, Electricity, and the Chemical Action of Light. New York: Harper & Brothers, 1844.