Around 1910, a group of Santa Fe railroad employees, a local school teacher, and Margaret Scott, a cousin of the Grand Canyon pioneer Emery Kolb, began holding Sunday School for their children in various homes before transferring to the one-room schoolhouse. The parents would gather to sing hymns and read scripture together. There were no regular church services, but parents would regularly check the hotel registers at the El Tovar Hotel and the Bright Angel Lodge to see if a minister had checked in, and if one was found, they would be asked to hold a worship service.

Around 1924, the first Community Building was completed, and Sunday School and church services were held there typically on Sunday evenings. Between 1924 and 1935, ministers from various denominations would often travel from Flagstaff and Williams, Arizona to lead worship services. These visiting ministers were provided a complimentary room by the Bright Angel Lodge, had meals provided by hosting families, and were allowed to keep the offering collection as payment for their services. In 1935, the first Community Building burned, and the present Community Building was erected, becoming the church home.

In 1937, a permanent church board was established with the aim of maintaining a Community Church, including the goal of having a chapel and a minister solely for the Grand Canyon. In 1947, the National Park Service provided an old Citizen Conservation Corps building and lot for the parsonage (the lot on which the present parsonage stands), and coupled with the assistance of the Santa Fe Railroad, Fred Harvey Company, and local residents, converted the building into the first Community Church parsonage.

During the summer of 1948, Rev. Kenneth Porray arrived from New York to assume the role of the first Resident Minister of Grand Canyon Community Church. Since that time, many resident ministers have served Grand Canyon Community Church and the greater Grand Canyon community. Revered annual Grand Canyon traditions such as the Easter Sunrise Service on the Rim, the Christmas Eve Candlelight Service, and the annual Christmas Bazaar can all be attributed to their origins with the Community Church.

Grand Canyon Community Church is unique in that its beginnings cannot be attributed to the pioneering or church planting efforts of a missionary or evangelist. Instead, its origins came from families who desired to have Sunday School for their children at the Grand Canyon. Today, after almost 90 years of ministry in Grand Canyon National Park, the Community Church continues to honor its legacy by providing an opportunity for people to come and worship at one of the most recognizable natural wonders of the world. It is lead by the Resident Minister and a church board consisting of lay leaders who are members and employees of the greater Grand Canyon community.