The very first record of Wickendorf, which includes Frankenhorst, dates back to a document written by Pope Clement III in 1189, in which he refers to the settlement as "Wickendörp". The farming village expanded quickly as it lay on the old Hansa route between Wismar and Dömitz.

Between 1770 and 1922, there were several brickworks and lime kilns on the site where Frankenhorst now stands. The clay and lime required as raw materials, as well as peat for use as fuel, were available in ample quantities. Many of the official buildings in the district of Schwerin were constructed using the building materials produced here.

At the beginning of the 1920s, there was already an inn for tourists called "Seelust" on the site. This restaurant was in the building which now forms part of the Best Western Seehotel Frankenhorst and is called "Haus 2" (House 2) or "Haus am See" (the House at the Lake). In the night of 17th to 18th October 1935, there was a fire in the attic of the "Seelust" inn. Nobody was hurt but the entire roof was burnt out. The attic was rebuilt and the venue remained in business for many more years, although during the Second World War, like many other buildings, it was put to another use.

In 1921, the writer Hans Franck bought the 30-acre property on the Ziegelsee Lake in the district of Schwerin. He loved the place, which he called Frankenhorst, and lived there for more than 40 years. The name he gave the estate comes from a combination of his own name "Frank" (as in "free" or "open") and "Horst", which means a "coppice" or "eagle's nest". After his death, the Frankenhorst was turned into a guest house for what was then the district of Schwerin. High-ranking guests from the district stayed there as well as veterans of East Germany's GDR party and other important figures. Erich Honecker himself obviously appreciated the place and he stayed there during the 1987 Farmer's Congress in Frankenhorst.

Following the reunification of Germany, the guest house began to offer accommodation and food for tourists and today it houses the 4-star Seehotel Frankenhorst.

In 2004, the land including the hotel was classified as a site of natural heritage. This gave the unique location an additional focal point. It is precisely the magnificent location of the hotel on the banks of the Ziegelsee Lake - which now lies in the middle of a landscape conservation area and a European bird sanctuary - that makes the Seehotel Frankenhorst a favourite destination for tourists and holiday makers as well as locals.