Mühledorf is first mentioned in 1364 as Mülidorf.
During the Middle Ages the village was part of the barony of Kramburg. In 1373 the village was donated to the Münchenbuchsee Commandery. In 1528, Bern accepted the new faith of the Protestant Reformation and suppressed the Commandery. Mühledorf came under Bernese rule and in 1533 was assigned to the court of Gelterfingen in the district of Seftigen created. The village has always been part of the parish of Kirchdorf.
The Gürbe and Müsche river projects of 1855-1911 drained the swampy valley floor and opened up farmland. It also made it possible to build roads to Belp and Rümligen. Today, agriculture is still the main industry. However, around two-thirds of the work force commute to jobs in nearby towns and cities.