After the fateful winter of 1791, which buried the village of Karvaičiai under sand, some residents relocated to Juodkrantė and began building a church. The first church was wooden and burned down in 1878 during the Midsummer celebrations. Seven years later, in August 1885, a new brick Evangelical Lutheran church was consecrated, designed by architect Friedrich August Stüler.
In the 18th century, most residents of the Karvaičiai parish, which included Juodkrantė, were Curonians and Lithuanians, and Juodkrantė's fishermen attended only Lithuanian services. By 1920, only 50 out of 367 Juodkrantė residents attended Lithuanian services.
After World War II, the church was closed. In 1976, after extensive renovations, it housed the Miniature Museum exhibition. In 1988, the church was returned to the Evangelical community, and since 1989 it has been rented by the Catholic community.