In 2001, he left Worldwatch Institute to establish the Earth Policy Institute, devoted to providing a plan to save civilization. At the Institute, his years of working on global issues through an interdisciplinary lens has enabled him to identify trends those working in specialized areas might not see. They have also allowed him to consider global solutions to the many environmental concerns of today. Some of the more important works Brown has written at the Institute include World on the Edge: How to Prevent Environmental and Economic Collapse (2011), Eco-Economy: Building an Economy for the Earth (2001), and the Plan B series. His most recent book is The Great Transition: Shifting from Fossil Fuels to Solar and Wind Energy (2015) co-authored with Janet Larsen, J. Matthew Roney, and Emily E. Adams.
In 2001 Brown suggested a "tax shifting" structure which would reduce income taxes and offset them with taxes on environmentally destructive activities such as carbon emissions. It would lead to an "honest market, he said, by adding a tax on carbon to pay for the hidden costs of climate change. It would also account for the environmental costs of things such toxic waste, the overuse of raw materials, mercury emissions, the generation of garbage, the use of pesticides, and the use of throwaway products such as plastic bottles, all activities that would be discouraged by taxing. He says that by keeping such environmental costs "off the books," and thereby hidden, society risks the same fate as a large company such as Enron, which failed immediately after auditors learned they had kept major costs off their books.
In May 2001, he founded the Earth Policy Institute to provide a vision and a road map for achieving an environmentally sustainable economy. In November 2001, he published Eco-Economy: Building an Economy for the Earth, which was hailed by E.O. Wilson as "an instant classic." In 2009 he published Plan B 4.0 and in 2011 World on the Edge. In 2012 he published Full Planet, Empty Plates.