Milner's contributions to Malay and Malaysian history extend through numerous books published by esteemed presses such as Cambridge University Press, Blackwell Press, and the Institute of Southeast Asian Studies in Singapore.
He later served as the Director of the Australia Asia Perceptions Project of the Academy of the Social Sciences in Australia which studied the role of cultures in international relationships, and produced three volumes of essays for Oxford University Press.
In 1995, Milner assumed the role of Basham Professor of Asian History at the Australian National University, later becoming the Dean of Asian Studies until 2005.
He holds the position of Emeritus Professor at the Australian National University and serves as International Director and Professorial Fellow at Asialink (University of Melbourne), focusing on Australia-Asia issues.