The name meant a humid place, a reference to the formation, at that time, of extensive marshes around the Ehle River.

In 955, Otto I is supposed to have founded Möckern's parish church, following his victory over Hungary on August 10 of that year.

By the 14th century, Möckern had become the property of Quedlinburg Abbey, which, with the town as a manor, the Count of Arnstein mortgaged.

In the 17th century, the town suffered heavy damage from an occupation in 1626 during the Thirty Years' War and a conflagration in 1688.

The relative prosperity of the town was reflected in the private construction that began in the second half of the 19th century and continued till the beginning of World War I.

The Hagen family lost the Möckern castle and a branch of the State Archives Magdeburg was installed there.

The castle, which remained town property, became Möckern's elementary school in 1998, after the state archives moved out.

In 2005, despite significant local protest, a remote facility for mentally incompetent criminals was established on a 12-acre (49,000 m2) former army base in the Lochow section of town.

In 2002 it absorbed Friedensau, Lübars, Stegelitz and Wörmlitz,[5] in 2003 Büden and Ziepel,[6] in 2004 Hohenziatz,[7] in 2007 Zeppernick,[8] and in 2008 Theeßen.

[9] On 1 January 2009 it absorbed the former municipalities Dörnitz, Hobeck, Küsel, Loburg, Rosian, Schweinitz, Tryppehna, Wallwitz and Zeddenick,[10] and on 2 July of the same year Magdeburgerforth and Reesdorf.