The first service of the newly formed St. John the Baptist Episcopal Mission Station in the Diocese of Atlanta was held on June 1, 1958, in the Clayton Community House (now the Rock House) in the town center of Clayton. About twelve people attended the first service.

Bishop Claibourne visited the church in 1959 and suggested that if church members were willing to change the name to St. James, he would transfer to them the treasury of the defunct St. James Church of Tallulah Falls. So the Mission Station of St. John the Baptist was dissolved and St. James Episcopal Church of Clayton, Georgia was established.

During the fall of 1960, St. James moved its services from the Community House to the vacated offices of Dr. Pete Lampros located on Savannah Street next to the farmer's market. While there, St. James was known as the "downtown storefront church." The building was remodeled in 1966 to accommodate growth.

The present 1.6 acre church site on Warwoman Road was purchased in 1976. In 1977 the present church building was designed. A construction contract with the local building construction firm Rabun Ridge, Inc. was awarded in early 1978, and construction began immediately. The first service in the new church building was held on Christmas Eve in 1978 and a formal dedication service was conducted on July 8, 1979. The active membership in 1979 was 56 communicants.

A 25th anniversary celebration was held June 5, 1983. At that time there were 115 members 84 who were active. In 2001, the Vestry made the decision for the church to become self-supporting.

The Rev. Stephen Hall came to St. James from Fort Dodge, Iowa on July 16,2006. He was installed and celebrated the 25th anniversary of his ordination in a festival service November 19 2006. Bishop J. Neil Alexander was the celebrant.

The St. James Vestry recently approved a plan for expanding the church and voted to initiate a capital campaign.

St. James has a very active outreach program. The church facilities are used daily by various community organizations. The Miracle Fund was established to help members of the community and others with significant monetary needs. An educational fund was also established to assist college students to meet expenses from anonymous donations.

The core membership of St. James is composed of a group of permanent residents. A number of parishioners have second homes in Rabun County and spend as much as 6 months in the area. Another group of people who attend St. James are the weekend people who have second homes and come to St. James when they are in the area. Additionally many visitors worship at St. James while on vacation in Rabun County. The St. James' congregation of today is positive in its attitude and open to change.

St. James holds two Sunday services - 8:00 am and 10:30 am. Both services include the Eucharist and a sermon.