The National Superintendent of the Year award was given at the American Association of School Administrators national conference Friday.
The winner was Roderick Paige, former superintendent of the Independent School District in Houston who is now the Secretary of the U.S. Department of Education.
Pedersen was one of the four national finalists this year. He is also the N.C. Superintendent of the Year.
Kim Hoke, spokeswoman for Chapel Hill-Carrboro City Schools, said the system is proud of Pedersen's accomplishments.
"It's a wonderful achievement (for Pedersen) to have been selected as North Carolina Superintendent of the Year as well as one of the four finalists for National Superintendent of the Year," she said.
Pedersen could not be reached for comment.
He has won numerous awards since he took the position in 1992 and serves on many education-related committees.
Pedersen is a member of the BellSouth Superintendent Leadership Network, president of the Chapel Hill-Carrboro Exchange Club and represents the school system as one of 15 districts chosen for the National Minority Student Achievement Network.
During the nine years under Pedersen's leadership, the percentage of students proficient on state examinations has risen to 92 percent, up from just 80 percent before his time as superintendent.