• Fr. Michael O'Brien, 1957-March 23, 1958 [upon death]
• Fr. John S. Whalen, April 1, 1958-June 1974
• Fr. William J. Amann and Fr. Charles Latus, June 1974-June 28, 1978 [Co-pastorate]
• Fr. William J. Amann, June 28, 1978-June 1981
• Fr. John J. Quinn, June 1981-June 25, 1991
• William Lum, June 25, 1991-July 16, 1996 [resigned, suspended]
• Sr. Kathryn Wahl RSM, July 16, 1996-Nov. 30, 1996 [Temporary administrator]
• Fr. Stanley G. Kacprzak, Nov. 30, 1996-June 25, 2002
• Fr. Robert L. Beligotti, June 25, 2002-June 2005
• Fr. Gary L. Tyman, June 2005-June 2008
• Fr. John F. Gagnier, June 24, 2008-June 30, 2010

During the 1950s, the Eastern Greece area was experiencing booming population growth thanks in large part to the growing presence of the Eastman Kodak Co. in the town. In response to an increasing number of Catholic families in the area, Bishop James Kearney established a new parish and named Fr. Michael O'Brien, formerly of St. Monica's parish in the city, as the founding Pastor. The parish would be named after Our Lady of Mercy, in honor of the Sisters of Mercy who were celebrating their 100th anniversary in Rochester in the year the parish was formed. Parish boundaries were redrawn with 250 families coming from Holy Cross, 250 from Mother of Sorrows, and 200 from St. Charles Borromeo. Six acres of land would be acquired at the corner of Denise and Armstrong for use by the new parish in May 1957.

The first Mass was celebrated on September 24, 1957, the fest of Our Lady of Mercy, at the former Lake Theater on Lake Avenue (today occupied by Charlotte Appliance). Masses would continue to be offered at this site for the next year until construction on the school and church was completed. Our Lady of Mercy was incorporated on October 4, 1957. Early the following year, on March 23, 1958, Fr. O'Brien died of a heart attack at a school registration event. He would soon be replaced by Fr. John Whalen, who was named Pastor on April 1st. Construction began on the school in May of 1958, and continued for several years in increments. The Sisters of Mercy would staff the school from 1958 through its closure in 1980.

On December 25, 1958, the first Mass would be celebrated at the new Our Lady of Mercy campus in the basement of the school. Mases would continue to be offered there until a temporary church was completed. Construction on this church began in 1961. The church would be attached to the school gymnaisum and seperated only by a retractable wall. This "temporary church," which was completed and ready for worship in 1962, would end up serving the community until the present-day Our Lady of Mercy church was constructed approximately 31 years later. The cost of the church building was $165,000. Construction on a permanent church was repeatedly delayed because of the large cost of operating the parish school.

Our Lady of Mercy purchased a temporary rectory at 617 Denise Rd and a convent at 603 Denise Rd. These properties would later be sold after further construction on the Mercy property created more permanent edifices for these needs.

By the mid-1990s, the parish began to raise money for the construction of a permanent 600-seat church building to replace the temporary church. LaBella Associates was hired to design the church. The new church would cost $1,700,000 and groundbreaking began in August 2001. On June 16, 2002, Bp. Matthew Clark joined the community to celebrate the dedication of the new Our Lady of Mercy church, which had been constructed on the site of the former temporary church. Around this time Mercy had 769 registered families, which was down from roughly 900 only a few years earlier. Attendance would continue to decline as the 2000s progressed, and soon there was talk by the Eastern Greece/Charlotte planning group to close Mercy. The parish would be clustered with nearby Holy Name of Jesus and start sharing a Pastor with them in June of 2008. A recommendation was made by the Greece/Charlotte planning group in 2009 that Mercy be closed and sold. Bp. Clark issued a decree to that effect, and a final Mass was offered on June 30, 2010. Today, the former cluster partner, Holy Name of Jesus, is also slated to close.