Brooks was a Resident Scholar at the School for Advanced Research in Santa Fe, New Mexico from 2000–2001, and later joined the staff as Editor of SAR Press.

His 2002 monograph Captives & Cousins: Slavery, Kinship and Community in the Southwest Borderlands focused on the traffic in women and children across the region as expressions of intercultural violence and accommodation.

He extends these questions most recently through an essay on the eighteenth and nineteenth century Pampas borderlands of Argentina in his co-edited advanced seminar volume, Small Worlds: Method, Meaning, and Narrative in Microhistory from SAR Press.

His 2016 book, MESA OF SORROWS: A HISTORY OF THE AWAT'OVI MASSACRE (WW Norton) earned the Caughey Prize for the most distinguished book on the history of the American West, and the Erminie Wheller-Voegelin Award for the best work of Ethnohistory from the American Society for Ethnohistory David Brion Davis commented when making the Frederick Douglass Prize second prize for Captives and Cousins: Slavery, Kinship, and Community in the Southwest Borderlands: "Until James F. Brooks, virtually all historians of American slavery have ignored the Spanish Southwest—the region acquired by the U.S. in 1848, as a result of the Mexican War.

Brooks portrays and analyzes forms of slavery and captivity among the Indians and Spanish that differed markedly from the Anglo-American bondage to the east.