With the Polish beet workers, who came to Lolland-Falster in big numbers around 1900, a need for Catholic church services followed with them. Already before 1911 church services were held in private homes or at Polish Barracks from time to time. Around 1911 four Dutch Franciscan conventuals acquired the work in the church at Lolland-Falster. With help from the sugar factory in Nakskov it was possible to have monthly services on the sugar factory. In February 1913 the Franciscan Establishment bought a property from the Danish Sugar Factories and architect Ewaldsen drew a tree church, which already was completed for the consecration on the 4th of May 1913.
On March 3rd 1917 the Saint Franciscan Establishment a villa at Bredgade and furnished it to a rectory. On the 30th of October 1919 Nakskov became an independent parish for the Catholic churches in Nakskov, Ravnsborg, Højreby and Rudbjerg Council.
The foundation stone for the Franciscan church, drawn by architect H.C. Glahn, was placed on April 22nd 1921, and the consecration took place on the 6th of November later that year. Thanks to the sugar factory in Nakskov, which donated the bricks from an old demolished farm, and the Poles’ efforts to clean the stones, the expenses for the construction of the church were restrained.
In 1924 Karen Juncker painted the pictures for the crossroads. In 1927 a statue of the holy St. Francis of Assisi was placed in the niche above the main entrance to the church.  It was executed by the sculptor Aksel Theilmann. The church got its first organ in 1923. It was a gift from the church in Fredericia. In 1923 an assembly hall was built for the church.
In 1926, on the occasion of the 700th anniversary of the death of St. Francis of Assisi, Saint Francis Church was decorated with chalk paintings executed by Birgitte West.
In the church an altar is found for Maximilian Kolbe (1894-1941). He is the Polish Franciscan, who died for a fellow prisoner at the concentration camp in Ausschwitz, who had a wife and kids. He was canonised in 1982, and his saint’s day is the 14th of August. His altar is memory of that Poles established the church. In 1981 a new parish hall was consecrated. It is drawn by architect Mogens Bech, Nakskov, and received the name Maksimilian Kolbe House.

The church was threatened with closure in 2016, but the diocese entered into a cooperation agreement with the Catholic school in Nakskov (Stenoskolen), which ensures continued church activity.

Sunday, November 7, 2021, the church's 100th anniversary was marked with a celebration mass by Bishop Czeslaw Kozon and a subsequent reception.