The Lawrence, Kan., school system initiative aims to address the problem of male students graduating at lower rates than female students.
The foundation said that it will reassess the prize given how urban education has changed in the last 13 years, but it was also disappointed with the "sluggish" performance in urban schools.
The proposal comes after the state board of education voted to take over Little Rock's schools.
The first independent analysis of Oakland, Calif., school district's initiative to support boys of color found that students enrolled in the program had better grades and school attendance rates and fewer suspensions than their peers.
The city's Independent Budget Office found that students with disabilities who attended charter schools were more likely to stay in their schools for four years than similar students in regular district schools.
City and school leaders hope the extra time will boost student academic performance, especially in the city's lowest-performing schools.
State education officials voted to immediately dissolve the city's elected board but to keep local superintendent on an "interim" basis.
Data from the National Center for Education Statistics show that in fiscal year 2012 the median per-pupil spending by local school districts declined by 2.5 percent.
Former Superintendent Heath Morrison resigned last year to care for his ailing mother, he said, but his departure came just days after an internal report recommended his termination.
The chancellor will replace the Bloomberg-era networks, which were run by independent organizations, with regional centers that superintendents will oversee.