Brooklyn College Academy was ranked second (tied with Benjamin Banneker Academy) for highest graduation rate in the borough of Brooklyn, with 97% of students graduating on time.

Brooklyn College Academy, founded in 1986 in a partnership between the then-Board of Education and Brooklyn College, served as an alternative school—a program which was created to help older high school students that have not done well in other settings.

Almost all of the school's graduates go on to attend college, two-year or four-year institutions.

Thomas was given the title of principal in 2019 following the retirement of previous principal, Nicholas Mazzarella, who began his career at Hostos-Lincoln High School in the Bronx and came to Brooklyn College Academy in 2005.

In 2015, the girls Brooklyn College Academy Bobcats beat the East Harlem Pride to win the Public School Athletic League's girls B Division city championship.