The school opened in August 2008 with an initial freshman class of 43 students, and operates within the Roman Catholic Diocese of Brooklyn.

In 2013 it moved to more spacious quarters in the East Flatbush neighborhood of Brooklyn.

In July 2011, Lourdes Academy was renamed Cristo Rey Brooklyn High School.

Its goal is to give children from low-income families a better chance for a college education, and assistance is available if they cannot pay the $2000 annual tuition.

In 2016, twelve students participated in the third annual service trip, this year to Nicaragua.