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 1987 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.

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 Evensong.

On June 30, 1926, Mr. Fleming retired after having served as Rector for a quarter of a century, and was designated Rector Emeritus.  On the occasion of Mr. Fleming's retirement he observed that he was "leaving an 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 subsequently 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. Rev. 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 Seaman’s' Church Institute, Manhattan. In 1968, Father Nugent's deteriorating health made it difficult for him to continue to shoulder the heavy duties and responsibilities of his office, and convinced him that it was in the common interest 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.

Following Father Batchelor’s resignation, Nativity was served by the interim priest The Rev. Dr. William Beckles and a number of supply priests including The Rev. Dr. Jeffrey Hamblin and The Rev. Ronald Lau.

“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, Brooklyn under The Rev. Edmund T. Alleyne who was appointed Priest-in-Charge in July, 1999.  The Church of the Nativity soon relinquished its parochial status and is now a mission congregation.

As times changed and as the two congregations became yoked the 8:00 am and 10:00 am services at Nativity were combined and from July 1999 when Father Alleyne assumed office, there was one Sunday service at 11:00 am.

In 2000, to mark the centenary of Nativity, members of the church led by Suffragan Bishop, The Right Reverend Rodney Michel on his visitation interred a time capsule on the church grounds. The capsule contained historical memorabilia, photographs and other items from parishioners.

On February 1, 2007, The Rev. Sheldon N.N. Hamblin was appointed Priest-in-charge. This ended the yoking arrangement with Holy Apostles Church. Since his arrival, much has changed. The Sunday service time now starts at 10:00 a.m. except during the summer when it is held at 9 a.m.  The management structure has also been changed and there is now a concerted effort towards the maintenance, appropriate use of, beautification and preservation of the building, as well as the establishment of a global mission ministry.   Under Reverend Hamblin’s leadership, Nativity is also now striving assiduously to regain its parish status.

Reverend Hamblin, as well as the Wardens, Bishop’s Committee and the rest of the Nativity family, is indeed grateful to all the past clergy and members who have helped to bring our mission to its one hundred and tenth year of ministry in the Brooklyn community and beyond.