Varaždinske Toplice were mentioned by King Bela III in a legal document.
In 1209 Varaždin was declared a free royal borough by the Croatian-Hungarian King Andrew II which allowed it to develop into the economic and military centre of northern Croatia. Due to the frequent Ottoman raids, the town was structured defensively around the old fortress, thus acquiring the shape of a typical medieval Wasserburg. As early as the 13th century the Knights Hospitaller (in Croatian Ivanovci) came to Varaždin, where they built a church and a monastery.
At the end of the 14th century the Varaždin fortress passed into the hands of the Earls of Celje. Over the following centuries Varaždin had several owners, the most influential being Beatrice Frankopan, Margrave Juraj of Brandenburg, who built the town hall; the last was Baron Ivan Ungnad, who reinforced the existing fortification. When at the end of the 16th century Count Toma Bakač Erdödy became its owner, assuming the hereditary position of Varaždin prefect (župan), the fortress remained in the ownership of his family until 1925.
In 1756, Ban Franjo Nadasdy chose Varaždin as his official residence turning Varaždin into the capital of all of Croatia. It hosted Croatian Sabor and the Royal Croatian Council founded by Empress Maria Theresa of Austria.
Reformation and the counter-reformation left a lasting mark on Varaždin. With the arrival of the Jesuits, the school and the convent were founded. Furthermore, a number of churches and monasteries were built in the baroque style. As Varaždin was the seat of many Croatian noblemen in 1756 it became the administrative center of Croatia. However, when the great fire of 1776 destroyed most of the town, administrative institutions moved back to Zagreb.
By the 19th century Varaždin had been completely rebuilt and expanded. Crafts and commerce, and later the manufacture of silk and bricks flourished resulting in the creation of the town's theatre, music school, and fire department.