The What Works Clearinghouse said that a study of district- and charter-run schools in Philadelphia did not measure those schools' academic growth against schools with similar achievement levels.
The Bentonville, Ark.-based organization continued its support for organizations that promote charter schools and school choice.
Eugene G. White, who has led the Indianapolis district since 2005, is originally from Alabama.
In exchange, the district must provide significant new protections to prevent the harassment of students who are perceived to be lesbian, gay, bisexual, or transgender.
Highland Park, a district of fewer than 1,000 students facing a large budget deficit, will have both an emergency financial manager and assistance from Detroit schools, which is also under emergency management.
A court ruling invalidated the state takeover of the struggling district, but the changes should not slow down plans to stabilize the school system, said Bridgeport schools chief Paul G. Vallas.
The District of Columbia school system is under investigation by federal and local officials based on allegations of test tampering.
The Highland Park district near Detroit is operating with a $11 million deficit, and may be placed under state control.
The foundation is expanding the number of judges who select the winner of the prize for high-performing urban districts.
The school board says that some top officials will no longer be required to live within the boundaries of the 157,000-student Texas district.