Obama has also chosen Colorado Sen. Ken Salazar to be interior secretary, according to an Obama transition source.
Duncan is currently in charge of the country's third-largest school district, and for the past seven years has focused on improving struggling schools, closing those that fail and getting better teachers.
Sources say the Duncan announcement will be made at Chicago's Dodge Renaissance Academy, an elementary school the two visited in 2005.
Duncan ran an education nonprofit on Chicago's South Side before working in Chicago Public Schools under former chief Paul Vallas, now the schools chief in New Orleans.
Obama's choice has been anticipated, and argued about, by education groups anxious to see what Obama will do to fix the country's ailing schools. Obama managed throughout his campaign to avoid taking sides in the contentious debate between reform advocates and teachers' unions over the direction of education and the fate of President Bush's No Child Left Behind accountability law.
The selection of Duncan may satisfy both factions. Reform advocates wanted a big-city school superintendent who, like Duncan, has sought accountability for schools and teachers. And teachers' unions, an influential segment of the party base, wanted an advocate for their members; they have said they believe Duncan is willing to work with them.
Salazar is a first-term Colorado senator who has established a name for himself on public lands and energy resources issues. He headed the Colorado Natural Resources Department from 1990 through 1994.
The Associated Press contributed to this report.