Fleischer received his PhD from Princeton University in 1982. After leaving Princeton, Fleischer held teaching posts at Washington University in St. Louis and the Ohio State University. In 1988, Fleischer was awarded a genius grant under the prestigious MacArthur Fellows Program. In 1993, Fleischer joined the faculty of the University of Chicago. Fleischer focuses primarily on Ottoman history, specializing in the Age of Suleyman. Currently he is working on a major work on Suleyman the Lawgiver as well as a number of papers dealing with the time period. In addition, he has begun work on Apocalypticism and its relationship to his field of study. Fleischer also sits on the editorial board of a number of publications, including the Cambridge Studies in Early Modern History and the International Journal of Middle Eastern Studies. Fleischer is also a past director of the University Chicago's Center for Middle Eastern Studies and a member of the editorial board of the Historians of the Ottoman Empire.
- "Shadows of Shadows: Prophecy in Politics in 1530s Istanbul," International Journal of Turkish Studies 13 (2007): 51-62.
- "A Different Sort of Scholar: 'Abd al-Rahman al-Bistami (d. 1454) and the Science of Letters," Festschrift Hans Georg Majer (Munich, forthcoming, 2000).
- “Seer to the Sultan: Haydar-i Remmal and Sultan Süleyman,” in Cultural Horizons. A Festschrift in Honor of Talat S. Halman, ed. Jayne L. Warner. (Syracuse: Syracuse University Press, 2001), pp. 290-99.
- "The Lawgiver as Messiah: The Making of the Imperial Image in the Reign of Süleymân," in Soliman le magnifique et son temps, ed. Gilles Veinstein (Paris: La Documentation Française, 1992), pp. 159-77
- "Imperialism and the Apocalypse, 1450-1550," (Annales, forthcoming).
- "Between the Lines: Realities of Scribal Life in the Sixteenth Century," in Studies in Ottoman History in Honour of V. L., eds. Colin Heywood and Colin Imber (Istanbul: The Isis Press, 1994), pp. 45-61.
- "Secretaries Dreams: Augury and Angst in the Ottoman Scribal Service," Armagan: Festschrift fur Andreas Tietze. Prague, 1994.
- "From Şeyhzade Korkud to Mustafa Âli: Cultural Origins of the Ottoman Nasihatname," in IIIrd Congress on the Social and Political History of Turkey. Princeton University 24-26 August 1983, eds. Heath W. Lowry and Ralph S. Hattox (Istanbul: The Isis Press, 1990), pp. 67-77.
- Bureaucrat and Intellectual in the Ottoman Empire: The Historian Mustafa Âli (1541-1600). Princeton, NJ: Princeton University Press, 1986.