Sixty-five cents and a dream were the Original seeds that were planted to begin the Agency. In 1892, a young lady deposited the sixty-five cents into an offering plate at a church meeting and made the statement that she would like the gift to grow and become an orphanage. It took several years for the money to grow to the point that the young lady's dream could become a reality.

The Agency was opened (as the Christian Orphanage) on January 28, 1907 by the Southern Convention of Christian Churches and was operated by this organization until 1931. At that time, the Congregational and Christian Churches merged, whereupon the Agency became an institution of the Southern Convention of these churches.

In February of 1964, the name was changed from the Congregational Christian Homes for Children to Elon Homes for Children Inc., because the Agency had become an institution of the newly formed United Church of Christ and one of the denomination's thirteen children's homes. At one time, the Agency had been the only childcare institution of the Southern Convention of the Congregational Christian Churches.

Boys Town of North Carolina was founded in Charlotte in 1970, merged with Elon Homes for Children in 1985 and soon added services for girls. The Agency has had to be aware of the changing needs of the communities, families, and young people it serves in order to keep the Agency's programs and services current and relevant. Since its incorporation in 1907, the Agency's primary purpose has been to serve dependent children, most recently in the areas of Foster Care, Behavioral Health Services, and Schools. The increased need for quality educational services prompted the agency to ramp up the enrollment in the Kennedy Charter School in Charlotte and to open a private, tuition based college preparatory school on the Elon campus. Consequently, the agency name was changed in 2008 to Elon Homes and Schools for Children, Inc.