Van Wagenen received her bachelor's degree at Vermont College in 1982 and her master's degree in Public History at New York University (NYU) in 1984. Ten years later she completed her Ph. D. in American History at NYU. Her doctoral dissertation was published as a book, Sister-Wives and Suffragists: Polygamy and the Politics of Woman Suffrage 1870-1896, in 2003. In October 2012 she received the Distinguished Alumni/Alumnae Achievement Award from the Graduate School of Arts and Sciences at NYU.