The church was a two-story apartment building purchased in 1957 by Father Ouyang Jingyu, a diocesan priest, in Lane 85, Tingzhou Road. With few parishioners, the living room doubled as the church. At the time, the area was sparsely populated, with residents belonging entirely to Wanshengli, hence the name Wanshengli Catholic Church. Nine years later, Father Ouyang passed away, and Father Cui Ruian took over. That same year, a severe storm flooded the entire second floor, prompting the bishop's office to sell the site and purchase the current one. At the time, the current building was vacant land, but a two-story building now stood in the courtyard, with the living room still serving as the church. In 1968, Father Cui returned to the Congregation of the Missionary Sisters of Patronage as spiritual director, and was succeeded by Father Li Boji.

In July 1968, Franciscan Father Su Li-an of the Order of St. Francis Xavier was entrusted with the management of the church. The following year, fellow Franciscan Father Fan Yi-cai arrived in Taiwan to assist. To further their evangelization efforts, the priests actively raised funds, and in March 1970, groundbreaking ceremony began on the current three-story building, which was completed in December of that year. The first floor served as the church, while the second and third floors housed men's apartments. The church was named after St. Francis Xavier, the patron saint of the order, and was renamed the Wanshengli St. Francis Xavier Church, a name it still uses today.

In 1972, the Xavier missionaries concluded their work in Taiwan and returned to Italy, where Father Li, the original priest, took over. By then, Father Li had suffered a brain injury from a car accident and traveled abroad for treatment in 1973. Father Wang Wensheng, parish priest of St. Francis Xavier Church in Mount Tai, took over. To promote missionary work, Father Wang invited his cousin's wife and cousin (known as Mother Wang and Uncle Wang) to assist the parish. To meet the needs of the time, he converted the men's apartment into a women's apartment.

In 1994, the Xavier Missionaries returned to Taiwan, with Father Bai Mingzhong in charge. They converted part of the apartment into the order's home in Taiwan and assisted the ailing Father Wang in parish affairs. After Father Wang Wensheng passed away in 1995, the Xavier Missionaries took over parish affairs, with Fathers Bai, Luo Jianzhong, and Wang Jingren successively serving as parish priests.

In 1995, plans began to transform the original two-story building into an activity center. However, God had His own plan, and although the activity center was lost, the beautiful courtyard remained. In 2000, renovations to the existing interior and exterior of the church, including the Marian Pavilion, were completed, and a Marian procession was held during the church's anniversary celebration that year.