The Holy Family initiative began with a small group of Catholic laity in Excelsior in August 1995. Four friends - Tom Steward, Theo Chalgren, Rob Roy, and Joe Morin - received the blessing of Archbishop Harry Flynn to build the first Catholic high school in the Twin Cities in more than 30 years. By early 1998, the project became Holy Family Catholic High School, one of the few laity-driven Catholic high schools developed and built anywhere in the country.
Groundbreaking occurred on May 25, 1999 with Archbishops Flynn and Roach, the school's Board of Directors, President Paul Stauffacher, community dignitaries, and a host of friends and supporters in attendance. Construction of the campus and facility began in July of 1999. The school opened on September 5, 2000, accommodating both freshman and sophomore students. Holy Family Catholic High School was formally dedicated on October 25, 2000, and in the spring of 2003, graduated its first senior class.
A Lasallian affiliation with the Midwest District of the Christian Brothers was formally established on October 19, 2005. The school was the first in the Christian Brothers' 300-year history to seek a formal affiliation without prior contact with a Lasallian ministry.