St. Jürgen’s Church was built between 1904 and 1907 as a neo-Gothic brick building according to the plans of the Prussian chief building officer Oskar Hoßfeld under the construction supervision of the Flensburg-based architect Alexander Wilhelm Prale. In the Middle Ages, a hospital for lepers and plague patients had stood on this site. The name St. Jürgen is derived from this hospital, as is the district name Jürgensby.

A special feature of this church is the position of the tower in the east and the choir in the west. The church forms a memorable silhouette to the town located in the valley on the fjord with the two round towers flanking the choir and the slender main tower, which determines the image of the eastern slope of the fjord.

Inside, a late Gothic net vault spans the hall building. The furnishings are characterised by the neo-Renaissance interior, which goes back to the Flensburg sculptor and founder of the Museum of Decorative Arts Heinrich Sauermann: including the gallery on three sides, the altar with the Hans Peter Feddersen painting of the „Homecoming of the Prodigal Son“ and the baptism. The Renaissance pulpit by the Flensburg sculptor Heinrich Ringeringk from 1602 was taken over from the Church of the Holy Spirit. The parish celebrated its services there from 1895 until the construction of this church.

The modern windows were designed by Ernst Günter Hansing in 1959. They replace the original windows, most of which were destroyed in June 1945 by an ammunition explosion in the port area near Kielseng.

In the church hang two ship models donated in 1904 and 1913. The tradition of donating a ship to the church is closely linked to life on the coast and the sea.

In 2014/15, the vault of the church, which had been damaged by cracks, had to be extensively renovated. The outer walls were braced with stainless steel rods. A large part of the costs was raised by the „Förderverein zur Erhaltung der St.-Jürgen-Kirche Flensburg e.V.“.