Frederikshavn Baptist Church was founded on 5 October 1860 and today consists of Frederikshavn Baptist Church, Skagen Baptist Church and the scout house "Gitte's House" in Jerup.
The congregation has its origins in Aalborg, Hals and Jetsmark Baptist circles, and at the foundation counted 162 members. In the years from 1869 to 1901 the congregation ran schools - in 1887 six schools with 4 teachers and 2 female teachers. The congregation thrived and later established circles in Skagen and Jerup. In 1901, the congregation was divided for the first time, and a new, independent congregation was established in Sæby, which at the time of its foundation counted 131 members. The congregation was divided again in 1934, when Sindal congregation was founded with 182 members.
The congregation bought a small house in Nørregade no. 15 in Frederikshavn as its first meeting place. The meetings were held here for the first few years after the purchase, but it soon became clear that it was too small for the purpose. Expansions were attempted, including the acquisition of a larger hall in Søndergade 20, where the Baptist Society's annual meeting was held in 1895 with an annual meeting ending in Plantagen, but there was a lack of a real church, and this was completed in Asylgade in 1896. It has since been expanded and modernized several times, the last time in 2013, when the church hall and parish hall were renovated with new colors and new decoration.