It's the first time the Broad Foundation has given that award to a charter school.
YES Prep began in 1995 to serve low-income students in the East End and it now serves over 5,000 students on ten middle and high school campuses.
YES Prep spokeswoman Trisha Cornwell says when kids begin as middle schoolers, the focus is all about getting into college.
"A lot of our kids come in two to three grade levels behind in basic skills across the board, math, reading, social studies. What we do is we really work on empowering our students to take the initiative in learning. And so we give them the resources and the support they need to catch up."
The Broad Foundation looked at student scores on state and national exams in granting the prize.