Ellen Johnson, president of American Atheists from 1995–2008, is an activist for atheist rights and the separation of church and state in the United States.

Johnson has been active in American Atheists organization since 1978. She describes herself as a "second-generation atheist" and a life-long atheist. Her educational background consists of Bachelor's Degrees in Environmental Studies and Political Science, and a Master's Degree in Political Science from The New School for Social Research.

Johnson took over as president in 1995 after founder Madalyn Murray O'Hair went missing along with her son and granddaughter (they were later found to have been abducted and murdered by two ex-convicts, one of whom, David Waters, worked for her organization).