The Županja area was permanently settled in the prehistoric period. The first settlements were created in the Neolithic period, on elevated beams and along numerous smaller streams. Those first people who lived in huts belonged to the holders of Starčevo culture. Although archaeological finds from this and later periods are meager, there is no doubt that since then this area has constantly been populated.
The oldest written record of Županja (Zapanablacia – Županje blato) is the Lazarus’ map of Austrian-Hungarian Empire published in 1528 in Ingolstadt. In 1536, the Ottomans set up a smaller military checkpoint with a ferry used for the transport of goods and local population on both sides of the river Sava. After the defeat of the Ottoman army in 1683 in Vienna, in autumn 1687 the army used the same ferry in Županja while escaping from the Austrian imperial army. Županje Blato remained as the 11th Company (part of the 7th infantry regiment) headquarters until the border demobilization. The domestic population was incorporated in the border system as well. All the men from 16 up to 60 years of age were subjected to strict rules of military service. In order to guard the border, along the Sava river blockhouses were built on wooden poles.
In 1717, Franciscans founded the Roman Catholic parish in Županje Blato and started building the Church of the Martyrdom of St John the Baptist. Since 1761, new houses have been built methodically, in rows. The first embankment on the river Sava was built in 1764. During the 18th century Županje Blato gradually formed as an increasingly important border place, but the population growth was stopped as a result of the plague in 1781. New parish church was built in 1800. In 1861 the National Library and Reading Room was established as well – the first in the Slavonian part of the Military Border. At this time, military and administrative discipline was weakening, which culminated in full demilitarization on August 8th 1873. 1n 1881 this area was finally linked with Banal Croatia.
Although there were no military operations in this area, Županja was hit hard by the Word War I. In the time of Kingdom of Serbs, Croats and Slovenes (Kingdom of Yugoslavia since 1929) Županja was the seat of a district that included Županja and 13 villages. During the Second World War Županja was spared from war operations. In the early post-war years nationalization was carried out, as well as forced collectivization, and the population was forced to give up their property and enter into new peasant cooperatives, many of which were left without basic assets for soil tillage.
Since 1963 Županja was officially granted a town status. The holder of social and cultural events in postwar Županja was the Public University. In 1953 the local history museum opened its doors to public, and in 1959 the area of the former barrel factory was transformed into a city park. In 1964 a branch of Matrix Croatica was established, and in 1969 began Radio Županja its broadcasting. The sixties were marked by a more intense urbanization and construction of road infrastructure.
In the nineties Županja went into the Croatian war history as the city with the longest uninterrupted period of general alert, which lasted for three and a half years. However, the people of Županja managed to adapt to the dangers of war and survive in spite of the devastating attacks. Owing to the administrative restructuring of Croatia, on the 29 December 1992 Županja acquired the city status.