In 1957, Pecora was selected as Chief of the Branch of Geochemistry and Petrology within the United States Geological Survey. He established programs in geochronology, experimental petrology, and mineralogy. In 1961, he returned to research. He was named Chief Geologist in 1964 and a year later was appointed Director of the United States Geological Survey by President Lyndon B. Johnson. As Director, he pressed for programs that would be responsive to emerging national problems, such as investigations of gold resources and off-shore oil and gas exploration. He established the National Center of Earthquake Research in response to problems revealed by the 1964 Alaska earthquake. As Director, he advocated for the creation of a remote sensing satellite that would be used to gather information about the surface of the Earth, which became the Landsat program, the longest-running project for gathering images of Earth from space. Pecora was director of the USGS when the Astrogeology Research Program began in 1963.