Stark was the first openly atheist member of Congress, as announced by the Secular Coalition for America.[42][43] Stark acknowledged that he was an atheist in response to an SCA questionnaire sent to public officials in January 2007.

On September 20, 2007, Stark reaffirmed that he was an atheist by making a public announcement in front of the Humanist Chaplaincy at Harvard, the Harvard Law School Heathen Society, and various other atheist, agnostic, secular, humanist, and nonreligious groups.[44] The American Humanist Association named him 2008 Humanist of the Year,[45] and he served on the AHA Advisory Board. On February 9, 2011, Stark introduced a bill to Congress designating February 12, 2011, as Darwin Day; this was a collaboration between Stark and the American Humanist Association. The resolution states, "Charles Darwin is a worthy symbol of scientific advancement ... and around which to build a global celebration of science and humanity."[46]

In 2011, he and eight other lawmakers voted to reject the existing national motto, “In God We Trust."[47] The next year, Eric Swalwell, his challenger in the Democratic primary campaign, criticized him for this vote.[48]

Stark served on the Advisory Board of the Secular Coalition for America.[49]