[4] Beacon was founded in 1993 by District Three educators Ruth Lacey and Stephen Stoll[5] as an alternative to the Regents Exam-based testing system in favor of portfolio-based assessment.

Over time, Beacon was forced to accept certain aspects of the Regents-based testing curriculum, and to abandon its portfolio-assessment system as the sole method of graduation, which had been the case until mid-1999.

Beacon now utilizes, in its own words, "traditional testing ... [but] our students' progress is largely assessed through performance-based projects, completed individually and in groups.

Students take the Advanced Placement exam at the end of the course, and have an opportunity to attain college credits.

[citation needed]For its first two years, the Beacon School was located inside Fordham University's Lincoln Center Campus.

The building, previously used as a book warehouse by the New York Public Library was sold to the School Construction Authority for $45 million in August, 2011.

Past destinations included India, Cuba, Spain, England, Ireland, Venezuela, France, Japan, Sweden, Costa Rica, Mexico, Mozambique, South Africa, and New Orleans.

Sports including fencing, softball, track, wrestling, bowling, basketball, Ultimate, soccer, cross country, and tennis form a part of the culture at Beacon.

In addition, the boys baseball team advanced to the 2019 Public School Athletic League (PSAL) AAA championship game.

The game was played in Yankee Stadium on June 4 and The Beacon School lost to Gregorio Luperon HS for Science and Math with a final score of four to five.

[19] In 2016, Beacon's delegation placed first among 174 schools from over 30 countries in the Global Classrooms Model United Nations conference.

The rankings, calculated based on data aggregated from the 30 most competitive Model UN conferences in North America, divide teams into groups by region and overall standing.

[22] The New York City Subway's Times Square–42nd Street and 42nd Street–Port Authority Bus Terminal stations, served by the 1, ​2, ​3​, 7, <7>​​, ​A​, ​C​, ​E​, N, ​Q, ​R, ​W​, and S trains, are located nearby.

Although the proportion of minorities increased, many parents felt the quality of the school's education — particularly support for students with special needs — had suffered.