In 1990, a Bible study was started in the village of Agat by a missionary as an outreach of Harvest Baptist Church. Brother Ron Thomson (missionary) later took the leadership and established a church with the local folks and some believers from the outer islands. When Brother Thomson became terminally ill and went to be with the Lord, Harvest Baptist Church requested that missionary Elwood Hurst come and take over the work. While the Hursts raised support, others served in the interim to keep the church going.

In June of 1992, the Hursts arrived and assumed the responsibility of the pastorate of the Lighthouse Baptist Fellowship. The church met in a storefront building in the village of Agat. Nine people, including the Hursts' family of three, attended the first Wednesday night service. The church continued to faithfully minister to the needs of the people in the southern part of the island. The name was later changed to Lighthouse Baptist Church. The church continued its preaching, teaching, nursing home ministries, meeting with troubled youth, and visitation. The congregation grew over several years with a combination of local folks, people from outer islands, and military families.

By the late 1990's, the church converted a container into classroom space and partitioned another room to provide additional classrooms; but the church quickly outgrew the space available. Through the faithful giving of God's people, they established a building fund which grew quickly. Through the grace of God and the help of a local business, the church purchased a two-acre tract of land in December 2002. God continued to provide; and, in 2006, the congregation began building. Through God's provision, the congregation completed, paid for, and moved into their new building in 2008. The church continued to grow and was blessed greatly.

Over the years, two men have pastored the work in the Hursts absence. Missionary Dalton Heath served in 2000-2002, and Pastor Jim Hershenhahn served for five months from September 2008 to January 2009. In January 2011, the Quinlan family arrived as missionaries to Lighthouse and co-labored with the Hursts until June 2011, when the Hursts left for furlough. Pastor Quinlan continues to see God's blessing upon the faithful folks at Lighthouse, and the church continues to grow.