In June of 1749, Harpswell, including the Neck, Sebascodegan Island and "other small islands," was set off from North Yarmouth by the Massachusetts General Court as a distinct and separate precinct and in 1758 was incorporated as a town. In 1765, the total population of Harpswell (exclusive of Indians) was 836 persons, 300 greater than Brunswick. The original Parish was established in 1751 under the name of the "Second Parish of North Yarmouth." In 1753 a church was organized, and the Reverend Elisha Eaton was ordained as its pastor. 

Under the leadership of Reverend Eaton, the original Meeting House was begun in 1757 and completed in 1759 or 1760. This Meeting House was in continuous use until 1844 and is still standing today. It has square pews and its high pulpit and old galleries are still preserved. The congregation worships there in June each year. In 1843, a new Parish was formed by several individual church members who combined for the purpose of building a new Meeting House. During the spring and summer of 1843, the church building now known as the Elijah Kellogg Church was built; and the dedication of this new Meeting House was held on September 28th of that year. 

The Reverend Elijah Kellogg was called as Pastor on April 25, 1844 and installed on June 18, 1844.  So began an affiliation that lasted, though not without interruptions, until Reverend Kellogg's death on March 17, 1901. The Harpswell Centre Congregational Church was renamed in his honor and is now known as The Elijah Kellogg Church, Congregational.

 
In 1965, the members of the church contributed their skills and labor to increase the size and functionality of the present Meeting House. A lower level was excavated and built to include classrooms and a fellowship area with a full kitchen. An extension was built on the east end of the building to include office space and restroom facilities.
 

In October 2001, a new and expansive Fellowship Hall was dedicated. The exterior was carefully planned and crafted so as not to detract from the integrity of the original historic structure. The functionality of Fellowship Hall and its meeting rooms has given the church a greater visibility and more active presence in the community. Along with increased church programming and use, the building has served as host and gathering place for the Harpswell Community Nursery School and a variety of non-profit and service groups in our town.