UNIS has an extensive Athletics program, running across three distinct seasons (Fall, Winter and Spring for students in 7th-12th grades, M3-Tut 4), and consists of 42 school teams. The Director of Athletics, Daniel O'Connor,  is responsible for the coordination and supervision of all UNIS teams.

UNIS is a member of New York State Association of Independent Schools (NYSAIS). UNIS Athletic teams participate in independent leagues including: Private Schools Athletic Association (PSAA), the American International Private Schools League (AIPSL), and New York City Athletic League (NYCAL).

UNIS also plays non- league games against other private, public and Catholic high schools throughout all five boroughs of New York.