The history of Lost Creek Presbyterian Church begins in 1759 when a Presbyterian Society, known as the Cedar Spring Church, was organized. A log meeting house was erected and this meeting house was in use until about 1799. The first official notice of Cedar Spring Congregation is found in the records of Donegal Presbytery, October 1, 1768 when the congregation made application for supply ministers. In 1795 the Presbytery of Huntingdon was formed and the Cedar Spring Congregation became a member of this new Presbytery. In 1799 the congregation decided to abandon the Cedar Spring building and erect two new meeting houses, one in Mifflintown and one in Lost Creek, to better serve its members. This movement to affect two separate congregations began in 1797 when Major Hugh McAlister and David Boles each donated a plot of ground, totaling 143 perches, from their adjoining farms. An agreement was entered into with Hugh Watt to erect a hewed log church on this ground, now know as the Lost Creek Presbyterian Cemetery located south of McAlisterville. Another meeting house was constructed in Mifflintown. The first official mention of the Lost Creek Church is found in the records of the Presbytery of Huntingdon on October 2, 1799 when the Lost Creek and Mifflintown congregations asked for permission to apply for supply ministers.

The log church built near McAlisterville in 1800 was used until about 1838 - 40 when a larger brick edifice was constructed near the same site. This structure was occupied until March 28, 1887, when the trustees decided it was no longer safe and was to far from town. The structure was razed and most of the materials were used in constructing the present structure now named Lost Creek Presbyterian Church. The new church was dedicated May 6, 1888. On April 8, 1875, The congregation at Mifflintown was granted a separate church Organization that is now known as Westminster Presbyterian Church. During the previous 75 years the two branches of the former Cedar Springs Congregation were one organization. One bench of elders served both branches of the church. They also shared the services of the Minister, with Mifflintown having three Sabbaths' preaching out of five, while Lost Creek received the services on the other two Sabbaths and paid two fifths of the pastor's salary. This arrangement continued until the division of the branches of the church . For the 13 years following the separation Lost Creek was without a regular pastor. The congregation, however, remained strong and active for it was during this time that they erected the present house of worship in the town of McAlisterville.

In 1960 the Presbyterian Church in the U.S.A. merged with the United Presbyterian Church in North America forming the United Presbyterian Church in the U.S.A. As part of this merger Lost Creek Church was transferred from the jurisdiction of Huntingdon Presbytery to Carlisle Presbytery. The building constructed in McAlisterville in 1887-88 remains basically the same. Some alterations have been made. New pews and a new floor were installed in 1939, and the education building was added in 1955-56. The most outstanding feature of the building is its stained glass windows. Constructed of leaded English miffled stained glass, which was noted for its rich jewel like colors, the windows were produced prior to 1860 and were carefully preserved and moved from the old building in the cemetery.