Meinisberg is first mentioned in 1332 as Meynesberg. The municipality was formerly known by its French name Montmenil, however, that name is no longer used.
The area has been settled since the Mesolithic and Neolithic ages, as finds near the Scheidwegen section of Meinisberg indicate. La Tène and Roman artifacts have been found near the Steinen section and a High Middle Ages wooden castle was found near Reibenwald. From the Late Middle Ages Meinisberg was ruled from Pieterlen which was under the authority of the Prince-Bishop of Basel. In 1816, it came under the authority of Bern and in 1833 became an independent community. At this time it was still part of the parish of Pieterlen. When the Nidau-Büren canal was built (1865–75), the Aare River now ran past Meinisberg. The community grew due to its location on the edge of the Naturschutzgebiets Häftli (Natural Park) and ease of reaching Biel/Bienne from Meinisberg.