See her memoir, This Child Will Be Great (2009).
Johnson took over as president in 1995 after then-president and 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).
In November 2002, Johnson announced the formation of the Godless Americans Political Action Committee (GAMPAC), a PAC to endorse political candidates who support the separation of church and state. She is the executive director of that organization.
Starting in 1994, she was the co-host of The Atheist Viewpoint, a television program, which is available "on dozens of cable systems throughout the nation and on the Internet."
On December 20, 2005 she appeared on an ABC special, "Heaven – Where Is It? How Do We Get There?", for which she was interviewed by Barbara Walters. She appeared on Larry King Live in April 2005, Good Morning America in December 2005, MSNBC's Scarborough Country on December 14, 2004, and appeared on Fox News three times in November and December 2003, and MSNBC's Phil Donahue.
On May 2, 2008 it was announced on the American Atheists blog that Johnson was leaving her post as President. On May 7, 2008, it was made public that Ellen Johnson was removed involuntarily by a vote of the board of directors. The reason was not revealed.