Our Lady of Good Counsel Parish was begun in 1855 as a mission of St. John's parish when a cornerstone of St. Lawrence Chapel was laid by Archbishop Kenrick. The Chapel of St. Lawrence O'Toole was later dedicated in 1859. In 1862, Fr. James Gibbons became the first pastor. In addition to his assignment to the Chapel of St. Lawrence Mission, Fr. Gibbons was also the pastor of St. Brigid and served as chaplain at Fort McHenry.  Each Sunday Fr. Gibbons crossed the Baltimore Basin, as the harbor was then called, at six o'clock in the morning, to hear confessions, celebrate Mass,

visit the sick and return across the harbor to St. Brigid in time to celebrate ten o'clock Mass.He was pastor until 1865. Fr. Peter McCoy, a protégé of Fr. Gibbons, was pastor from 1866-1885. He consolidated the parish and got it ready for a resident priest. At the same time, Fr. McCoy built St. Mary, Star of the Sea church.

Fr. Hagan, a classmate of Cardinal Gibbons, became the first resident pastor at St. Lawrence Chapel. During this time, immigration from Ireland was at its peak. While most of the immigrants passed from Baltimore to points further west, many took up residence where their feet first touched land in America, Locust Point. To provide for the religious needs of the additional people, Fr. Hagan planned for a new church to be built. Parishioners, including grain trimmers and waterfront workers, excavated the foundation for the church. The cornerstone for Our Lady of Good Counsel was laid and blessed in 1889 by its former pastor, Cardinal Gibbons. During the first year of the new church there were 62 baptisms. Fr. Hagan served as pastor from 1886 until his death in 1897.

Between 1897 and 1929, Our Lady of Good Counsel was served by four pastors: Fr. James Donellan Marr, 1897-1903; Fr. John Paul White, 1903-1904; Fr. Edward Augustine Williams, 1904-1908; and Monsignor Robert J. Achstetter, 1908-1929, who became pastor at Our Lady of Good Counsel at the age of 30.

In 1929, Fr. Francis Schwallenberg became pastor. He was able to keep the parish from foundering during the Great Depression and built a modern eight room school house. The school population grew so much that classes had to be held in the basement of the Church as well. The School Sisters of Notre Dame replaced the two lay teachers who had begun the school. In 1972, the school was closed and merged with the previously closed Holy Cross School and the St. Mary, Star of the Sea School to become the South Baltimore Area Community School. In 1982, this consolidated school became the Catholic Community School of South Baltimore.

Over the years, the pastors of the parish made improvements to the church building, including those to the interior of the church, the church hall, and renovations of the church kitchen. Handicap accessibility was enhanced, upgrades to the rectory were undertaken, and changes to the steeple and bell tower were also made. From 1947 to present, the pastors at Our Lady of Good Counsel included: Fr. Edward Braham, Fr. John McGlone, Fr. Herbert Derwart, Fr. Henry Milkowski, Fr. John Barbernitz, Fr. David Smith and Fr. Raymond Martin in 2000. In 2002, the three parishes of Holy Cross, St. Mary, Star of the Sea and Our Lady of Good Counsel came under direction of Fr. Martin, forming the Catholic Community of South Baltimore, though each still a separate canonical parish. Fr. Patrick Carrion succeeded Fr. Martin in January 2008.