In September of 1987, the Archdiocese of Dubuque requested that metropolitan locations study areas for increased cooperation and collaboration. Over the course of the next three years, many joint discussions were held between the LaSalle and Regis Boards of Education regarding implementing a single administration to govern the Catholic secondary schools in Cedar Rapids. During a joint meeting on February 7, 1990, the LaSalle and Regis boards voted to merge into a central Catholic high school (corporate votes are received at this time and Archdiocesan approval is granted).
On November 3, 1990, the capital campaign to raise funds for the new central high school begins along with Mount Mercy Board of Trustees approving the purchase of Regis High School for $1,000,000. In a joint board meeting in February of 1991, the LaSalle and Regis Boards reject the proposal for a united administration. Despite a reorganized fund drive being initiated in the Summer of 1991, the drive is suspended in February 1992.
On May 3, 1994, Archbishop Daniel Kucera issues a letter to all Catholics in the Cedar Rapids area requesting that the LaSalle and Regis boards form a joint school board. On August 25, 1994, the Cedar Rapids Metropolitan Catholic Secondary Board of Education conducts its organizational meeting. It assumes all governing responsibilities for Regis and LaSalle High Schools. Later that year, Novak Design Group is hired to conduct a building analysis to determine a possible location for a new high school. On February 23, 1995, the Regis-LaSalle Board of Education passes a resolution concluding that it is not in the best interest of Catholic Education in the Cedar Rapids-Marion area to continue operation of two secondary school locations. Additional community discussions are held throughout 1995. In February of 1996, the board passes a resolution to construct a new high school if adequate financial support exists.
Ground was broken on the construction of Xavier High School on June 22, 1997 with Archbishop Jerome Hanus present for the occasion. Xavier officially opened its doors for its first day of school on September 2, 1998 to 700 "Saints" and with Jeff Henderson, former Regis-LaSalle Chief Administrator, as its principal.
Novak Design Group served as the building architect with Taylor Ball as the general contractor. The central element of Xavier's design is its chapel (named for Monsignor Ardell Sodawasser) which features striking stone crosses on its exterior and beautiful stained glass on its interior. The stained glass features a nautical theme in honor of Xavier's patron saint, Saint Francis Xavier, who was a Roman Catholic missionary to Asia. Xavier features 27 general classrooms, 15 special classrooms/labs, a 440-seat theatre (named for Xavier's predecessors, Regis and LaSalle), a 2,000-seat competition gymnasium (named for supporter, Ron Thillen), a 4,000-seat football stadium, and a 240-seat cafeteria. Xavier sits on 60 acres of land, bordered by 42nd St. (South), Usher's Ferry Rd. (East), Highway 100 (North), and the Rock Island Preserve (west). Xavier's campus also features competition baseball (named for Ken Charipar), softball (named for Bob Erusha), and soccer (named HECO Field for Highway Equipment Company) facilities along with tennis courts and an 8-lane all-weather track.
Tom Keating, former Activities Director at Dubuque's Wahlert Catholic, was named Xavier's principal for the 2004-2005 school year as Jeff Henderson was named the new superintendent of schools for the Archdiocese of Dubuque. During Keating's tenure, Xavier emerged as a premier Catholic secondary school in Iowa, re-dedicating itself to its Catholic identity and its commitment to excellence in the areas of service, academics, and activities. Father Dustin Vu, who served as Xavier's chaplain from 2008-2020, played a key role in the areas of faith formation and vocational awareness.
In 2013, Xavier moved to a 1:1 Digital Learning Environment whereby each student was equipped with an iPad as a learning tool. In 2016, Xavier upgraded its Library Media Center (LMC) thanks to a generous donation from Mike and Jo Cambridge and Xavier Parents for Xcellence (XPX). That facility now features spaces for collaborative learning including "The Cube" (modular classroom) and the "iLab."
The 2018-2019 school year brought several significant changes to Xavier in its governance and daily student schedules. Xavier moved to the “President-Principal Model” of school governance, creating the position of “president” to better align the efforts of Xavier High School and the Xavier Foundation (responsible for fundraising and development). Tom Keating was named the first president in Xavier’s history in the spring of 2018. Angela Olson (previously Xavier’s associate principal) was later named the school’s new principal. Also starting with the 2018-2019 school year, Xavier adopted block scheduling, which led, among other positive outcomes, to more project-based learning opportunities for its students. Students would alternate between days of four extended class periods (i.e. an “A Day” would consist of Classes 1-4, while a “B Day” would consist of Classes 5-8).
Chris McCarville (R97) was named Xavier’s second president in the spring of 2019 following Tom Keating’s departure to assume the role of executive director of the Iowa High School Athletic Association.
In 2020-2021, Xavier launched its "Community System." This system helps build relationships with God and with others in addition to enhancing a sense of belonging and connection for each and every Xavier Saint who walks through our doors. The system is comprised of five separate “communities,” each of which will feature a cross section of 9-12 Grade students, teachers and staff. The communities themselves are named after various saints: St. Catherine of Siena, St. Juan Diego, St. John Paul II, St. Teresa of Calcutta, and St. Pio of Pietrelcina (Padre Pio).
In 2023, Xavier named former All Saints Elementary School principal, Lynn Holverson, as its fourth principal XHS principal, Angela Olson, assumed the role of Head of School at Iowa City Regina.