Franeker was founded around 800 as a Carolingian stronghold. The name probably derives from Froon-acker, meaning "country of the king"; the oldest street in the city is still called Froonacker. Beginning around the 11th century, Franeker developed into the administrative center Westergoa.
Franeker received city rights in 1374. In the 15th century, Albert, Duke of Saxony established himself in Franeker. The city appeared for a time to be growing into the primary city of Friesland, but was eventually overshadowed in this role by Leeuwarden.
During the period of the Dutch Revolt, the town sided early on with William I.