Thackston is a graduate of Princeton's Oriental Studies department, where he was a member of Princeton's Colonial Club, and Harvard's Near Eastern Studies department (Ph.D., 1974), where he was Professor of the Practice of Persian and other Near Eastern Languages since 1972. He studied at Princeton under Martin Dickson and at Harvard with Annemarie Schimmel. Thackston retired from teaching at Harvard in 2007.
His best-known works are Persian and Classical and Qur'anic Arabic grammars and his translations of the Babur-nama, the memoirs of the Mughal prince and emperor Babur, and the memoirs of Emperor Jahangir, or the Jahangir-nama. He has also produced important manuals or editions of texts in Levantine Arabic, Ottoman Turkish, Syriac, Uzbek, Luri, and Kurdish.
- "Harvard University Department of Near Eastern Languages and Civilizations: Graduate Student Handbook 2007-2008" - lists EMERITUS/RETIRED FACULTY: Wilson Bishai, Frank Moore Cross, Richard N. Frye, James Kugel (senior associate), Thomas O. Lambdin (senior associate), Muhsin Mahdi, William L. Moran, A. I. Sabra, Annemarie Schimmel, Wheeler M. Thackston, Jr.
- The History of Akbar, Volume 1 (the Akbarnama), by Abu'l-Fazl ibn Mubarak, edited and translated by Wheeler Thackston, Murty Classical Library of India, Harvard University Press (January 2015), hardcover, 656 pages, ISBN 9780674427754
- Jahangir, Emperor of Hindustan (1999). The Jahangirnama: Memoirs of Jahangir, Emperor of India. Translated by Thackston, Wheeler M. Oxford University Press. ISBN 978-0-19-512718-8.
- Professor Thackston's Sorani and Kurmanji Kurdish grammars
- Thackston, W. M., ed. (1989), A Century of Princes: Sources on Timurid History and Art, The Aga Khan Program for Islamic Architecture at Harvard University and the Massachusetts Institute of Technology, ISBN 092267311X
- The Emperors' album: images of Mughal India, an exhibition catalog from The Metropolitan Museum of Art (fully available online as PDF), which includes an essay by Thackston