Tetradrachmas of Philip II of Macedon found in Kratovo and might suggest that there was a settlement here even in those times.
In Roman times on the place of present day town there was a settlement called Tranatura. There was a mine nearby and the town was the seat of local authorities. No remains of the settlement was found but remnants of Roman fortification were found on Zdravce kamen hill above the town.
In 1153 Arab geographer al-Idrisi mentions the town of Koritos (or Koritas) and adds that it is wealthy and well populated. A charter of Byzantine emperor Alexios III from 1199 mentions the bishop of Koriton. In all probability the wealth of the town came from its mines.
The golden age of Kratovo started after in 1282 it became part of Serbia. Soon afterwards here settled Saxon miners who already worked in other parts of Serbia. The town was first mentioned under present day name in 1330. Gold, silver, lead, iron and copper were mined in the immediate vicinity and in wider surroundings of the town.
In the age of Emperor Dusan the mines of Kratovo were the prime source of wealth of Despotes Jovan Oliver. After his death, in the times of the fading of Emperor Uross authority, the town came into hands of Dejanovic family. Konstantin Dejanovic minted his silver coins here. The already existent colony of traders from Dubrovnik grew larger and took over the best part of trading with ores.
In 1389, during his attack on Prince Lazar, Ottoman sultan Murad I stopped in Kratovo to gather information and hold a war council. Next year, in 1390, his son, Bayezid, captured it from the Dejanovics and put his official (emin) to reside here. Kratovo was the seat of a nahiye, as a part of the sanjak of Velbuzd, as well as a kaza, seat of a kadi/judge, engulfing not only the towns vicinity but also Stip, Kocani and Nagoricani.
In the 15th century Kratovo was a very important mining town, inhabited by many wealthy and educated men, such as the writer Dimitar, or Marin, son of the priest Radonja, who in 1449 donated the whole sum needed for the fresco painting of the Prohor Pcinjski monastery. In 1484 Jovan Konic and Stepan, son of Branko, both from Kratovo, paid an amazing 16,424,000 akce for a three year rent of mints in Novo Brdo, Skopje and Seres. As a trade center Kratovo was also settled by Sephardic Jews. Kratovo was an important stop for Ottoman sultans: in 1455, before an attack on Novo Brdo, the Ottoman army regrouped here.
In the 16th century Kratovo ranked among the most important mining towns in the European part of the Ottoman Empire. The mint was opened in Kratovo in the last decade of the 15th century and immediately it became the second largest producer of coins in the Ottoman Empire (just after Novo Brdo), making mostly silver akce, and later gold coins as well. However from 1520 to 1540 minting and mining were in great crisis and many of the tenants, all of them local Christians, could not pay their leases and were imprisoned. Also, between 1519 and 1530 the number of Christian households dwindled from 982 to 606. After the reform and codification of the craft, the mining and minting recovered around mid-century. In 1550 C. Zeno noted in his travelogue that the Ottoman sultan gets 70,000 ducats from Kratovo. The official accounts of that year tell of benefits of 1,111,555 akce. However, due to the opening of new mints, this fell down to just 573,099 akce in 1573.
The mines were managed by their renters who held the title of a duke (knez). Most of them were Christians. Amongst these wealthy men who were the first among all men in Kratovo we find Dimitrije Pepic with his brothers or Andrija and Nikola Bojicic, who gave money for renovation of many churches around Macedonia (for instance Lesnovo Monastery). The inhabitants of Goldsmiths and Minters quarters (mahale), both Muslims and Christians, were businessmen who were famous for their investments in opening new mines such as Kucajna, Majdanpek or Kremkovica, or for leasing mints in other centers, for instance in Novo Brdo.
Such activity continued in early 17th century, but later in that century, around 1660 when Kratovo was visited by Evliya Celebi the mint has stopped its operation. The town was commanded by an ayan. Seven mines were active, yielding mostly silver and copper, but a lot of ore was brought from Osogovo and mountains around Kjustendil. Minors were locals who for their works in mines enjoyed certain freedoms and did not have to pay any taxes. Catholic bishop of Skopje Petar Bogdani reports in 1685 that Kratovo has 300 houses and 8 strong towers. At the time Kratovo was also famous for its copper products which were considered to be the best in the Ottoman Empire.
During the 16th, 17th and 18th centuries, under the Patriarchate of Pec, the bishops of Kjustendil often call themselves also „of Kratovo“ and some of them resided here as well since it was a more important and richer town than their seat.
In 1689 town was taken by the advancing Habsburg forces. However, they soon retreated and Kratvo was burned down in retaliation. A lot of people left the town together with the Habsburg army; in early 18th century we find some of them living in the Serb suburb of Buda (today a part of Budapest). After this disaster most of the mining activity in the area was taken over by Zletovo and Probistip.
It seems that the mining recovered only in the first half of the 19th century. In 1829 a local aga managed the mines. However, mining was now done on a much smaller scale: Amu Bue in 1836 found only two furnaces working, both in bad condition, and some 5,000 – 6,000 inhabitants. Later in that century the work was carried out by forced labor force recruited in villages from the region and many families have left the area because of it. The mines were finally shut down in 1882. At the end of the century the town population dwarfed to 4,500, more than half Muslim Turks.
In 1905 Kratovo had a Bulgarian lower grammar school and two primary schools while the Serbs had two primary schools. Each community held one of town churches.
The town was taken by the Serbian army on 9 November 1912. In following years the Turkish population left the town so that in 1931 the number of inhabitants was just 1,833.