Hayner has worked as a consultant at the Ford Foundation and the Office of the United Nations High Commissioner for Human Rights. She also served as a program officer for the Joyce Mertz-Gilmore Foundation, where she focused on international human rights and global security.
In 2001, she co-founded the International Center for Transitional Justice (ICTJ), an international human rights NGO. She directed this organization’s work on Sierra Leone, Peru, Ghana, and a number of other countries.
Hayner has written widely on the subject of truth-seeking. In 2001 she published the book Unspeakable Truths: Confronting State Terror and Atrocity, examining the work of over 20 truth commissions worldwide.