An organizational meeting for the establishment of the Nativity Mission was held on March 3, 1899. The first services were held in rented space at 1978 Nostrand Avenue and 1477 Flatbush Avenue.

On May 1, 1900 lots on Kenilworth Place were purchased, on which a church building costing more than $7,000.00 was erected later the same year. On January 4, 1901 the Reverend Andrew Fleming was appointed as Minister-in-Charge, dividing his time and energies between St. John's, Parkville and the Nativity Mission. The Mission was incorporated as a parish on May 20, 1901, being admitted into union with the church in the Diocese of Long Island on May 21, 1901. The Reverend Andrew Fleming was then elected as first Rector on May 29, 1901.

Changes in the development of the neighborhood led Mr. Fleming and the Wardens to the conclusion that the Kenilworth Place property could not be the permanent location of the church. Although various locations were studied and discussed, the more the subject was considered, the more unanimous became the conviction in favor of a site on Ocean Avenue. In the Spring of 1905, the present location on Ocean Avenue and Farragut Road (then known as Avenue F), was bought. But even after its purchase, there were serious obstacles to its development that had to be met and overcome before the construction of a new church building could proceed. However, thanks to the exertions of Mr. Fleming, the restrictions were finally removed in February 1909.

The ground-breaking ceremony for the present church was held on October 31, 1909, followed on November 28, 1909 by the laying of the cornerstone by the Bishop of Long Island, Dr. Frederick Burgess. The Building Committee selected plans submitted by Messrs. Dodge and Morrison, and engaged Mr. Rufus A. Brown as the general contractor.

The Kenilworth Place property was sold at public auction for $10,150.00 on January 11, 1910. The last service in the old church took place on April 24, 1910. Our present church building was opened for public worship on May 1, 1910.

The first World War absorbed much of the time and energy of the Rector and members of the parish, preventing the implementation of plans for the expansion of the church's mission and ministry. During this time the Red Cross Auxiliary enrolled eighty members and raised $3,000.00 for Allied War Relief projects. Fifty seven men from the parish entered the service and their names are listed on the Parish Honor Roll in the Narthex.

Following the war, the church continued its mission and ministry in Flatbush and on November 30, 1924, the burning of the mortgage took place at a service of Evenshon.

On June 30, 1926, Mr. Fleming retired after having served as Rector for a quarter of a century, and was designated as Rector Emeritus. On the occasion of Mr. Fleming's retirement he observed that he was "leaving and organization of splendid workers, a church property and building with furniture and beautiful materials worth more than one hundred thousand dollars, and having a spiritual value to the donors and workers beyond any measurement in dollars and cents."

The second and third Rectors of the Church of the Nativity, the Rev. R. Maxwell Bradner (1926-1929) and the Rev. Charles P. Holbrook (1929-1932), served for relatively brief terms of office of approximately two and a half years each.

In May 1932, the Rev. Thomas L. Settle was appointed as interim Rector, and was sbusequently elected as the fourth Rector, assuming office on October 1, 1932. Under his capable and energetic leadership, the Church of the Nativity continued its ministry during the difficult years of the Great Depression World War II, and the post-war period. Mr. Settle's resignation was tendered and reluctantly and regretfully accepted by the Vestry on July 6, 1950.

On April 1, 1952, the Vestry extended a call to the Rev. Charles F. Nugent, who was at the time a member of the staff of the Seamans' Church Institute, Manhattan. In 1968, Father Nugent's deteriorating health made it difficult for him to continue to shoulder the heavy duties and responsibilites of his office, and convinced him that it was in the common interst for him to retire. His resignation was received by the Vestry on June 30, 1968.

The sixth Rector, the Rev. E. Edward Batchelor, assumed his duties on November 1, 1968, having previously served as Rector of Holy Trinity Church, International Falls, Minnesota. Father Batchelor demitted office on Sunday May 14, 1995 after twenty seven years of faithful service to the Church of the Nativity.

For the next three years, the parish saw an influx of supply clergy performing sacerdotal roles and functions as the wardens and vestry of the period strove 'to keep the doors open.'

'Where there is a will, there is a way' as the saying goes.  After much deliberation and several meetings led by the Archdeacon of Brooklyn the Venerable Canon Michael Harris and his successor the Venerable Canon Peter P. Golden, the Church of the Nativity entered into a yoked relationship with the Church of the Holy Apostles, Windsor Terrace. The Rev. Edmund T. Alleyne was then appointed Priest-in-Charge in July, 1999. The Church of the Nativity soon relinquished its parochial status and is now a mission congregation in the Diocese of Long Island.

It is worthy to note that at the turn of the century (2000), members of the parish led by Suffragan Bishop, The Right Reverend Rodney Michel on his visitation interred a time capsule on the church grounds. Containing historical data, memorabilia, photographs and other items from parishioners, it is hoped that the capsule will be unearthed some time in the year 2025.