In 1888 the Church in Everglades City began as a Methodist church and was located at Halfway Creek pastored by Rev. George Gatewood.  After Rev Gatewood left the church various denominations of intenerate preachers were dispatched to  the small church until 1913. The church was then destroyed and services were moved to the Everglades Schoolhouse.  Another church was erected and used as a school and it too was destroyed.  In 1925 Rev. Gerrett Koyker established the church as Presbyterian. In 1926 Rev James Glenn was the pastor of the Everglades Presbyterian Church and the congregation held services in the Community House with the exception of hurricane flooding in 1926 and a fire in 1927,  and until the construction of the now standing building.
In May of 1939 the estate of Barron Gift Collier, founder of the county which bears his name donated land for the construction of a church. The gift came with two conditions; one, it had to be completed before October 1, 1940 and two it was to be non-denominational.  Both criteria were met when the dedication took place on May 5, 1940.
​The church was constructed with ship lap siding, a tin roof and Dade County pine flooring.  The Breezeway and  a fellowship hall were added in the 1950s. 
In 1990 a digital carillon was installed and chimes hourly and can be heard throughout the small town of Everglades City.
On September 4 Everglades City proclaimed the church to be a historical site.  In 2008 the bell tower and narthex were repaired. In 2010 the church went under complete restoration while celebrating its 84th birthday.  
Through the years, this little church has seen a number of pastors who would come from Naples and Fort Myers to lead the congregation.  In March 2006 Pastor Bob Wallace began his service at Everglades Community Church and is currently pastor for the attending congregation.