Science on the Ballot began as Science Debate, co-founded in 2007 by Matthew Chapman, Shawn Lawrence Otto, Chris Mooney, Lawrence Krauss, Austin Dacey, and Sheril Kirshenbaum. Michael Halpern and Darlene Cavalier joined the organization shortly after. The primary reason for starting Science Debate was in response to the near absence of science and technology topics in the presidential debates and in the campaigns. Within weeks of its founding, people and organizations from across the political spectrum signed the following petition:

"Given the many urgent scientific and technological challenges facing America and the rest of the world, the increasing need for accurate scientific information in political decision making, and the vital role scientific innovation plays in spurring economic growth, we call for public debates in which the U.S. presidential and congressional candidates share their views on science and technology, health and medicine, and the environment."

Supporters included prominent institutions such as the American Association for the Advancement of Science (AAAS) and the U.S. National Academies, as well as political strategists ranging from John Podesta, President Bill Clinton’s former chief of staff, on the left to Newt Gingrich, former House Speaker, on the right.