The cornerstone for Emmanuel Church's original building in Phoebus was laid April 11, 1897, formed from a mission of St. John's Episcopal Church to provide a church for the people of Phoebus. Mission work began earlier in 1878, by the Rev. J. J. Gravate, Rector of St. John's, assisted by Rev. Mayo of Newport News. In 1885, a church school was organized with seven families initially meeting in their homes. Later, the school met in a variety of places, including the private school operated by the Misses Jane H. and Elizabeth H. Bryan. Worship services were conducted mostly by missionaries.

A new church was eventually planned under the encouragement of the Rev. C. B. Bryan, Rector of St. John's in 1893. The name "Emmanuel" meaning, "God with us" was chosen. A parish hall was later added to the church facilities in 1914. Much of the interior work in the first Emmanuel Church, including the beamed arches, and pews, was done by Native American students at Hampton University. Some of these furnishings, including the altar table and font, are still in use by the church today.

Emmanuel grew steadily through these early years, served by borrowed clergy, retired priests, and lay readers. It remained a mission until 1947. In 1950, a Parish Day School was founded with the Rev. R. S. Little as Headmaster. The Rev. Little became the first Rector in 1951. By 1954, 170 students were enrolled and 400 were on the waiting list. The day school continued until 1974.

During the 1950s, Emmanuel experienced additional growth. In 1955 the property on Military Road (later to become Mercury Blvd.) was purchased. The original church property was sold to another denomination as the new church was built. Sadly, the first Emmanuel Church burned to the ground in 1969. The Rev. John Howard became the Rector in 1957 and the new facilities, consisting of what is now the present parish hall, at 179 East Mercury Blvd. were dedicated by Bishop Rose on October 5, 1958.

Emmanuel Church continued to grow after the move from Phoebus. A new capital campaign was begun in 1961 and by April 18, 1965, on Easter Sunday, the current Emmanuel Church was dedicated by Bishop Gunn. 

In 1972, the Rev. Howard Saunders became the Rector and served the parish until 1989. During this period, in 1981, an educational wing was added to the original facility. The Rev. Thomas Daily served as Rector from 1991 to 1993. Following this brief tenure, the Vestry called the Rev. Richard L. Vinson as the "Time-Certain" Rector to guide the parish in a new phase of growth and service. In 1997 Emmanuel celebrated its Centennial with year-long celebrations and a capital campaign. Nearly 20% of the campaign was designated for the local HELP Center. The remaining funds were used for both exterior and interior renovations including the parking lot, chancel and parish hall. In 1998, a call was issued to the Rev. Dr. C. Derek Pringle who served Emmanuel for 12 years and retired in September 2011.  Our current rector is the Rev. Rhonda E. Wheeler who started in January 2013.