Pekka Hämäläinen specialises in early and nineteenth-century American history and has particular interest in Native American, environmental, and borderlands history. His 2008 book The Comanche Empire received awards including the Bancroft Prize, the Merle Curti Award, the Caughey Prize, the Norris and Carol Hundley Award, the John C. Ewers Award, the William P. Clements Prize, the Kate Broocks Bates Award, the Great Plains Distinguished Book Award, the Philosophical Society of Texas Award of Merit, and Recognition of Excellence Award in the Cundill International Prize in History.
He is currently working on a book that traces the history of power relations and social worlds in North America from the seventeenth through the nineteenth century, integrating indigenous and European perspectives, borderlands and imperial histories, and transatlantic and continental approaches. For 2014–19, he has gained a European Research Council Consolidator Grant (€1,988,584) for the major research project "Nomadic Empires: A World Historical Perspective".
- "Of Lethal Places and Lethal Essays," with John R. Wunder, American Historical Review 104 (Oct. 1999), 1229–1234.
- "The Rise and Fall of Plains Indian Horse Cultures," Journal of American History 90 (Dec. 2003), 833–862.
- When Disease Makes History: Epidemics and Great Historical Turnings Points, ed. (Helsinki: Helsinki University Press, 2006).
- The Comanche Empire (New Haven: Yale University Press, 2008). Spanish translation by Peninsula Press in 2011; French translation by Anacharsis Éditions in 2012. Turkish translation by Alfa Publishers in progress.
- "The Politics of Grass: European Expansion, Ecological Change, and Indigenous Power in the Southwest Borderlands," William and Mary Quarterly 67 (April 2010), 173–208.
- Major Problems in the History of North American Borderlands, ed. with Benjamin H. Johnson (New York: Houghton Mifflin Company, 2011).
- "Lost in Transitions: Suffering, Survival, and Belonging in the Early Modern Atlantic World," William and Mary Quarterly 68 (April 2011), 219–223.
- "On Borderlands," with Samuel Truett, Journal of American History 98 (Sep. 2011), 338–361. Lead essay in JAH special issue, "Margins to Mainstream: The Brave New World of Borderlands History."
- Империя команчей. Введение: Колониализм наоборот. Reprinted Russian translation of the introduction to The Comanche Empire. Ab Imperio Quarterly: Studies of New Imperial History and Nationalism in Post-Soviet Space (Aug. 2012), 25–43.
- "The Futures of Native American History in the United States," Perspectives on History: The Newsmagazine of the American Historical Association 50 (Dec. 2012), 44–45.
- "What's in a Concept? The Kinetic Empire of the Comanches," History and Theory 52 (Feb. 2013), 81–90. Author's response in a book forum on The Comanche Empire.
- "The Shapes of Power: Indians, Europeans, and North American Worlds from the Seventeenth to the Nineteenth Century," in The Contested Spaces of Early America, ed. Juliana Barr and Edward Countryman (Philadelphia: University of Pennsylvania Press, Apr. 2014), 31–68.
- Liberty, Equality, Power: A History of the American People. With John M. Murrin, Denver Brunsman, Paul E. Johnson, Alice Fahs, Gary Gerstle, Emily S. Rosenberg, and Norman L. Rosenberg (Boston: Cengage, 2015).