The free royal town of Mirotice was established in the second half of the 13th century close to an old market village by the last Premyslids after the royal castle Zvikov and the royal town of Pisek were founded. The church of St. Jilji was built there, in Roman style early in the 13th century, and its administrator was instituted directly by the Czech kings.

Due to an economic recession after the Hussite wars, Mirotice started loosing its independence. The town, with all its privileges, was given to noblemen Pribik of Zahradka and Ondrej of Rasenice, by King Sigismund (Zikmund) in 1431. By 1457 the town was owned by the noble family of Lev of Rozmital. The once free Mirotice, now ruled by the royal administration, had become a subjective townlet.

Mirotice became part of the administration of the royal castle Zvikov in 1544. The Mirotice townsfolk founded their own city hall in 1562 in memory of their lost independence and as an expression of their ambition to gain back their lost autonomy. Svamberks of Zvikov favoured their town belonging to the castle. Therefore, Jindrich of Svamberk confirmed upon Mirotice in 1549, the privilege of using the town brewery, the municipal forests and the Lomnice River. Other privileges included; the right to use the municipal book of records and contracts, the town emblem (the first Premyslid sign-a female eagle), the communal brick-kiln and the municipal weighing machine. The written privilege also stated that there was a subjective duty to Zvikov, the feudal lord. One had to give him 180 days of service and pay various kinds of tributary; including 142 hens a year. In 1575, the auspicious economic development of Mirotice was slowed down due to a big fire, which destroyed 50 houses.

Mirotice remained a part of Zvikov after the partition of Svamberk's domain in 1584. There were 76 houses, mostly in the hands of the class and executive nobility. The economic situation of Mirotice was, at the beginning of the 17th century, so good that the Mirotice burghers contemplated the possibility of buying their once lost freedom back. In 1610 they agreed to pay 10,000 threescore of groschens to the Zvikov domain landowner, Jan Jiri Ehrenreych of Svamberk, to get out of their fiefdom. Unfortunately Pasov soldiers raided Mirotice in 1611 and ravaged the town to such an extent that the last instalment could not be paid. Mirotice was encumbered with debt and Jan Horcic of Prosty on Bratronice became the new owner. He granted the city all Svamberk's former privileges and even added some others.

The beginning of the thirty years war and the anti-Hapsburg revolt was disastrous for Mirotice. Most of the town's houses were plundered and burned to the ground. Ten years later, in 1630, there were 28 uninhabited houses of the former 83 in the town. The last third of the thirty years war completed the disaster. The town suffered as soldiers incessantly moved through demanding food, lodging, fresh horses, and ransom. The number of uninhabited houses was increasing as residents fled the town and left their homes. The main source of municipal income, the Brewery, was wrecked. This unhappy situation; characterized by a total decline of trade, a small number of inhabitants, and many houses in ruin, continued until the end of the 17th century.

Mirotice was in the possession of many owners in the 17th century. The last of them were Jiri Frantisek Doudlebsky and his wife Ludmila. They added the town to their neighbouring Cerhonice homestead. As well as the previous owners, they did not want to accept the ancient Mirotice privileges. This resulted in frequent lawsuits. In 1688, the Cerhonice homestead, including Mirotice, was bought by the Premonstratensain Monastery in Schlagl, Upper Austria. The lawsuits continued with the new owner until Emperor Leopold ended them in favour of Mirotice.

Mirotice's economic situation improved during the first decade of the Premonstratensian rule. Some uninhabited houses were reconstructed, trade activity was revitalised and even the municipal economy improved with the reopening of the town's brewery and the brick-kiln. This economic upswing brought danger of Germanization, because the new owner allotted the remaining uninhabited houses to German inhabitants from the Upper Austrian domains (mainly from the town of Aigen and its surrounding area). However, influence from the new German speaking inhabitants turned out to be quite weak, and the newcomers were soon assimilated under the influence of all the Czech environment.

The Austrian-French war, occupation by the French army for six months in 1741 through 1742, and the 14 day French army occupation during the Prussian war in 1744, caused a lot of damage to the area. However, Mirotice and the surrounding country were able to recover.
The Corporation of Mirotice worked well in the 18th century. Ancestors of the distinguished painter Mikolas Ales took part in the Corporation for the first time in 1742, soon they were elected aldermen and mayors. During this period of the 18th century, Mirotice achieved a good standard of living. Thanks to good revenues from the municipal brewery, its surrounding forests, the brick-kiln, and prosperous trade in local business. The lively traffic on the so called Imperial Road through Mirotice, played an important role for the welfare of many local inns. These quickly growing businesses were mostly in the hands of the local Jewish community. At the end of the 18th century Mirotice was enlarged by new homes on Rybarska street and the new quarter Neradov, built on the other bank of the Lomnice River.

Famous Czech marionettist Matej Kopecky married into a Mirotice family in 1795. He settled there after soldiering in the Napoleonic wars for several years. In 1817 he used to set off with his marionettes from Mirotice on long trips around Bohemia to play the theatre, which was very popular among the ordinary people. He was a big part of the Czech National Revival Movement. His theatre promoted Czech national pride and love for the Czech language.
The Mirotice municipality was established in 1792 by an experienced legal counsel who was an exponent of the state and responsible for political and judicial affairs.
1811 was a disastrous year for Mirotice. One of the town mills was destroyed by fire. It spread quickly and consumed the whole northern part of the square.

The push for autonomy known as the Czech National Revival, (a cultural and political movement to revive the Czech language and culture), influenced social life in Mirotice in the 1930's. Frantisek Ales, (father of the distinguished Czech painter Mikolas Ales who was born in Mirotice in 1852) and the sons of Matej Kopecky were active members of a newly founded theatre club. In 1869, the Society of Sokols and voluntary fire fighters were established by Ladislav Stroupeznicky. (Stroupeznicky was a Czech dramatist and novelist who later became the first dramatic adviser of the National Theatre in Prague.)

Mirotice social and intellectual life consisted of several societies and clubs during the second half of the 19th century. A reading group with 38 members and lead by the professional teacher Vaclav Spala, was established in 1888. A fellowship of veterans formed in 1882, a voluntary fire brigade was formed in 1883 and a gymnastic society was started in Sokol in 1900. Sokol played an important role in reviving personal and national consciousness. Its objective being to promote not only Czech culture and social life but physical, cultural, and intellectual development among its members.

Unfortunately in 1875, the fame and importance of Mirotice inns faded away. The busy traffic of its main road decreased when a newly built railway bypassed Mirotice and passed through nearby Cimelice and Smetanova Lhota.

The end of World War II brought tragic consequences to the small town. On April 29, 1945 an American aeroplane fired on retreating German troops of the Schorner Army and accidentally demolished 27 homes and damaged 30 others. 17 people lost their lives that Sunday morning.
Unfortunately the bombing was not the last of misfortunes in the centuries long Mirotice history of trials and tribulations. Supported by the Soviet Army and Soviet influence, both of which were already strong in Czechoslovakia, the communists were able to carry out a coup in February of 1948. For Mirotice, as well as for the whole country, it meant decades of communist rule. It will take many years before the town fully recovers from the forty years of the totalitarian rule, ended by the Velvet Revolution of 1989.