Public school Okanagan Mission is ranked 17th, while Vancouver's University Hill is slightly lower at 18th, ranking jointly with private schools Kelowna Christian and King David.
Private school York House rated the highest, with a perfect score of 10 out of 10, followed by Crofton House, Southridge, St George's and West Point Grey.
The Fraser Institute suggests private schools score better, because they are more accountable to parents.
The institute also found 26 secondary schools across B.C., including 21 public schools, have seen their academic performance improve over the past five years.
It also found 42 of the schools it measured fell further down the rankings list.
The lowest ranked secondary schools in the province were jointly Century International in Vancouver, Kumsheen in Lytton and Nisga'a in New Aiyansh.
The Report Card rates 284 public and independent schools based on several factors, but primarily on mandatory provincial exams in grades 10 through 12.
It also includes information about each school’s make-up, including parents’ average income, the percentage of ESL students and the percentage of special needs students.
The British Columbia Teachers' Federation has argued schools should not be ranked based on standardized testing.