[2] When it first opened, the school was based in St. Paul's Highland Park neighborhood, with K-6 students housed in a church building.
The rented building was at 426 Osceola Ave S. In 2012 all grades moved to a permanent location in Victoria Park, near the Mississippi River.
Nova's extracurricular programs include varsity sports, forensics (including mock trial, debate and model UN), robotics, art, theater, yoga, yearbook, newspaper, student senate, fencing, choir, chess, movie club, game coding, GSA and philosophy club.
Between 2012 and 2019 Nova won 28 conference championships in six sports (baseball, volleyball, basketball, cross-country, track, and soccer).
Eleven Nova graduates play Division 3 NCAA sports throughout the country in baseball, soccer, lacrosse, track, and cross-country.
In 2013, Nicholas Zinos sued Nova for violating his sixth-grade daughter's right to freedom of speech after she was stopped from distributing anti-abortion materials at school.
[14] The lawsuit was successful, and Nova was required to pay $8,000 in legal fees and allow Zinos's daughter to continue distributing the materials.
[15] On March 24, 2016, David and Hannah Edwards filed a charge of discrimination with the City of St. Paul Department of Human Rights alleging that Nova failed to provide an environment for their daughter to "undergo a gender transition... in a safe and timely way."