The Pulitzer Prize for Explanatory Reporting was first introduced in 1998, replacing the earlier Pulitzer Prize for Explanatory Journalism. It is awarded for a distinguished example of explanatory reporting that illuminates a significant and complex subject, demonstrating mastery of the subject, lucid writing and clear presentation.

• 1998: Paul Salopek , Chicago Tribune, for his enlightening profile of the Human Genome Diversity Project, which seeks to chart the genetic relationship among all people.
• 1999: Richard Read, The Oregonian (Portland, Oregon), for vividly illustrating the domestic impact of the Asian economic crisis by profiling the local industry that exports frozen french fries.
• 2000: Eric Newhouse , Great Falls Tribune (Montana) , for his vivid examination of alcohol abuse and the problems it creates in the community.
• 2001: Staff of the Chicago Tribune, for "Gateway to Gridlock," its clear and compelling profile of the chaotic American air traffic system.
• 2002: Staff of the New York Times, for its informed and detailed reporting, before and after the September 11th attacks on America, that profiled the global terrorism network and the threats it posed.
• 2003: Staff of the Wall Street Journal, for its clear, concise and comprehensive stories that illuminated the roots, significance and impact of corporate scandals in America. This was originally nominated in the Public Service category, but was moved by the jury.
• 2004: Kevin Helliker and Thomas M. Burton , Wall Street Journal, for their groundbreaking examination of aneurysms, an often overlooked medical condition that kills thousands of Americans each year.
• 2005: Gareth Cook , The Boston Globe, for writing about stem cell research.