Woodard is the author of six works of non-fiction. His first book, Ocean's End: Travels Through Endangered Seas, appeared in 2000. His most recent, Union: The Struggle to Forge the Story of United States Nationhood was published in the spring of 2020 and named a Christian Science Monitor Book of the Year.
He is a Visiting Senior Fellow at the "Pell Center for International Relations and Public Policy" at Salve Regina University and State & National Affairs Writer at the Portland Press Herald and Maine Sunday Telegram. He received a 2012 George Polk Award for an investigative project he did for those papers and was a finalist for the 2016 Pulitzer Prize for Explanatory Reporting for a series on climate change and the Gulf of Maine. He received a 2004 Jane Bagley Lehman Award for Public Advocacy (for his global environmental reporting), the 2012 Maine Literary Award for Non-Fiction (for American Nations), the 2016 Maine Literary Award for Non-Fiction (for American Character) and a Pew Fellowship in International Journalism at the Johns Hopkins University School of Advanced International Studies. Woodard was also a finalist for the 2016 Chautauqua Prize (for American Character) and for a Gerald Loeb Award for Distinguished Business and Financial Journalism in both 2013 and 2014. In 2014, The Washington Post named him one of the "Best State Capitol Reporters in America" and the Maine Press Association chose him as Journalist of the Year.His third book, The New York Times bestseller The Republic of Pirates, was the basis of the 2014 NBC drama Crossbones, written by Neil Cross and starring John Malkovich. Woodard was also a historical consultant for Assassin's Creed IV: Black Flag, which was also set in the time period covered in Republic of Pirates.
He was a long-time foreign correspondent of The Christian Science Monitor, San Francisco Chronicle, and The Chronicle of Higher Education, and has reported from more than fifty foreign countries and seven continents, from postings in Budapest, Hungary; Zagreb, Croatia; Washington, D.C.; and the US–Mexico border. His work has appeared in dozens of publications including The Economist, The New York Times, Smithsonian, The Washington Post, Newsweek/The Daily Beast, Bloomberg View, The Guardian, Washington Monthly, and Down East, where he was a contributing editor. He is currently a contributing editor at Politico.