It was through the efforts of a longtime resident of Gates Mills, Mrs. Ruth Isabel Strong (1879-1968), a devout Episcopalian who converted to Catholicism in 1942. Wartime restrictions limited gasoline and thus curtailed the opportunities for church attendance by those living in rural communities. For those Catholics residing in Gates Mills and its environs the nearest Catholic Churches were St. Gregory, South Euclid and St. Mary, Chardon. Mrs. Strong made an offer to the Bishop of Cleveland, Joseph Schrembs, for the use of the library-garden room of her home on Old Mill Road as a temporary chapel. This arrangement would afford Catholics in the Gates Mills area a convenient center for regular worship.
The conversion of Mrs. Strong’s library-garden room into a chapel was completed in December 1942 and 48 residents of Gates Mills and surrounding area attended the first Mass offered by Father Joseph Lamontagne, S.S.S. (1902-1982), Superior of the Blessed Sacrament Fathers in Cleveland. The Blessed Sacrament Fathers consented to the request of the now Archbishop Schrembs to service the chapel as a temporary arrangement.
By late 1943 it was evidenced that this Mission chapel had so developed it should have a name.  Mrs. Strong suggested in a letter to Bishop Edward Francis Hoban, who arrived in Cleveland to become Coadjutor to the ailing Bishop Schrembs, since birds, including larks, were in the area all year it might be suitable to place the congregation under the patronage of St. Francis of Assisi.  It was fairly certain that the Mission would become the first parish established by Bishop Hoban. On Wednesday, 11 August, 1943, Bishop Hoban notified Father William Bertram Gallagher (1902-1986) of his appointment as the first pastor of St. Francis of Assisi Parish.
In 1945 Mrs. Strong sold the house. Bishop Hoban advised parishioners to worship at St. Clare Parish, Lyndhurst which had been established on 18 September 1944. This arrangement encouraged Father Gallagher and his faithful band to locate a property suitable for the building of a church and rectory. His efforts were rewarded on 7 March, 1946 with acquisition of Sub Lots 1 & 2 on the south side of Mayfield Road close to SOM Center Road. With intense fundraising and planning the Cleveland architectural firm, Walker & Weeks was retained to design the church.
Groundbreaking for the church was performed by Father Gallagher on Thursday, 12 June 1947.  By late June 1948 the church was completed and the surrounding area landscaped with the rectory ready for occupancy at the end of September. On Sunday, 27 June 1948, Fr. Gallagher blessed the new edifice. On Sunday 3 October, 1948, Bishop Hoban came to dedicate the new church.
St. Francis of Assisi School was opened on Monday, 13 September, 1954 with children arriving by bus from Chesterland and Novelty in Geauga County. Initial enrollment was close to 170 pupils. The school consisted of nine classrooms, a Principal’s office, clinic, Teachers’ room and Multi-Purpose room, which also served as a cafeteria. The school expansion was completed in October 1960.
The Sisters of Notre Dame were to staff the new school. As a temporary measure, one classroom and the Teachers’ room became the living quarters for the five sisters. On Sunday, 10 October 1954, Archbishop Edward F. Hoban blessed the school. The Convent was completed and the sisters moved in on Saturday, 15 November 1958.
The present church was completed in September 1969. Bishop William M. Cosgrove, Auxiliary Bishop of Cleveland consecrated the altar. Four weeks later, Bishop Clarence G. Issenman, Bishop of Cleveland, blessed the church.
Monsignor Gallagher retired on 2 January, 1973 and continued to live in the rectory devoting his time to the sick at Hillcrest Hospital until he died 6 January 1986. Father Sylvester W. Fridrich was appointed the new pastor on 15 January 1973 and installed on 11 February, 1973.
Since the opening of the new church in October 1969, the first church continued to be used for weekday services including weddings and funerals. From Holy Week (7-14 April) of Eastertide, 1974 all services were held in the new church. The first church was cleared of its liturgical furniture and converted into a gymnasium thus enabling the all- purpose room in the school be developed into a library and multipurpose learning center. Among the events occurring during the fiftieth anniversary year of the founding of the parish was the Solemn Dedication of the church by Bishop Anthony M Pilla, Bishop of Cleveland, on Sunday, 3 October 1993.
Father Sylvester Fridrich retired as pastor of St. Francis of Assisi on 14 August, 1996 and Father James L. Caddy was named the new pastor on 15 August, 1996. Father Caddy was installed as the third pastor on Sunday, 20 October 1996 by Bishop Anthony M Pilla.
On Sunday 26, July 1998 there was a groundbreaking ceremony for the building of our Parish Center. Bishop A. Edward Pevec served as Celebrant. In 1999 with plans for the construction of the Parish Center it was time now to demolish the first church and the former rectory which was serving as the Parish Office. With the departure of the Sisters of Notre Dame there was some modification to the convent which was now to become the Parish Office. The Parish Center was dedicated on 12 April, 2000. The Center houses the school administrative offices, clinic, meeting room, cafeteria, gym, chapel, pre-school room, two kindergartens, art room, music room, and concession stand and maintenance.