As the place name Stöckheim also occurs in the city of Braunschweig and the district of Wolfenbüttel, it is difficult to determine which Stöckheim is mentioned in the medieval documents. The place name Flachstöckheim, which is commonly used today, first appeared in a church visitation report from 1590.
Since the middle of the 14th century, the development of the village has been closely linked to the knightly family of the Barons of Schwicheldt, who had their ancestral seat in Flachstöckheim for 500 years. The estate they built with its landscaped park still characterizes the image of the district today. In 1350, the brothers Hans and Heinrich Schwicheldt were enfeoffed with a farm and five hooves of land in Flachstöckheim by Bishop Heinrich of Hildesheim in order to protect the border with Brunswick, which ran close to the village.
The von Schwicheldt family influenced life in the small village on the Fuhse for several centuries - the four farmers, four half-horsemen and eight cottagers listed in the inheritance register of 1579 were all subject to service and duties to the von Schwicheldt family.
Industrialization reached Flachstöckheim at the beginning of the 20th century: in 1905, the brothers Max and Hermann Grumpel, whose Hanoverian banking house played a major role in potash mining, founded the Friedrichroda trade union and bought up mine fields in the Flachstöckheim and Ohlendorf districts. After the first test drillings had produced promising results, shaft sinking began and potash salt was mined between 1919 and 1924.
On October 1, 1937, the Reichswerke Hermann Göring took over all mining activities in the Salzgitter area. They built the Wortlah shaft a few hundred meters to the east to exploit the iron ore deposits. Today, only an ore wagon on the village square and a few opencast facilities that have since been put to commercial use are reminders of the mine, which was shut down on February 1, 1966.
Civic involvement is very important in Flachstöckheim. The local clubs have joined together to form an association, a support association takes care of the maintenance of the estate park and the clubhouse of FC Flachstöckheim is something of an unofficial village community center for the approximately one thousand inhabitants of the district, which belongs to the town of Südost.