At a Sunday Mass in May 1942, during the course of World War II, the pastor, Angelo R. Cioffi, urged his congregation to build a shrine dedicated to Mary, under her title of Queen of Peace, for the safe return of the men of the parish and country from the battlefields of the war and for a just and lasting peace. The parishioners accepted the challenge and vowed to erect the church. A building fund was then established which included plans for the projected shrine, as well the construction of a new convent, and the enlargement of the parish school.

Ground was broken for the construction of the church on October 3, 1948, with the cornerstone being blessed on October 29 of the following year by Raymond Kearney, auxiliary bishop of the diocese. The church was completed in 1950, built in the style of the Italianate Renaissance Revival architecture, and an image of Mary was enthroned over the main altar. It was built entirely in marble from various parts of Italy, with two pulpits, after the manner of Italian cathedrals. A large painting of the church's patron saint done by the noted artist Ilario Panzironi was installed over the main altar. The shrine was dedicated on August 15, 1951, by the Bishop of Brooklyn, Archbishop Thomas E. Molloy.

After the blessing of the cornerstone of the church in 1949, Cioffi had asked the people to donate their own personal jewelry in order to give thanks for the successful conclusion of the war by the creation of two gold crowns to honor further the planned image of the church's patroness and her son. The parishioners and other faithful began to donate wedding rings and other types of jewelry to the project. The collected valuables were entrusted to the firm of DeNatale Brothers in Manhattan so that the crowns and stars could be made, a process which took three years. The image was honored on May 24, 1952, by the addition of two diamond-studded crowns attached to it, which had been personally blessed by Pope Pius XII in Rome when they were presented to him in a special audience by Cioffi and the jeweler, Mr. DeNatale.

In more recent years, Regina has continued to grow with the support of the Catholic Church. Pope Benedict XVI elevated Regina Pacis to a Minor Basilica on October 19, 2012.

On December 8, 2012, the Most Reverend Nicholas DiMarzio, Bishop of Brooklyn, celebrated a Solemn Mass inaugurating Regina Pacis as a Minor Basilica.

On the Solemnity of All Saints, November 1, 2015, His Excellency Nicholas DiMarzio, Bishop of Brooklyn Blessed the new Saint Joseph Chapel and Dedicated the Columbarium.