Representatives of the Dutch East India Company (VOC) first encountered Kupang in 1613 after having conquered the Portuguese fort on the island of Solor.

At this time the area of the city was governed by a Raja of the Helong tribe, who claimed descent from the island of Ceram in the Maluku archipelago.

Kupang occupied an ideal strategic position to exercise control over parts of Timor since it was possible to monitor shipping activities along the south coast of the island from the location.

However, by 1646, the VOC was firmly established on the nearby island of Solor and renewed their agreement with the local Raja of Kupang.

[6] In January 1653, a Dutch fortification, Fort Concordia, was built on an elevated position on the left bank of the river estuary.

After a series of defeats were inflicted on the Dutch between 1655 and 1657, large groups of refugees from the neighbouring VOC allies of the Sonbai and Amabi principalities settled into the vicinity of Kupang and formed small polities on land that had traditionally belonged to the Helong.

The area of the town was also settled by various indigenous groups from the region, and by mardijkers (who were the descendants of freed slaves under Dutch jurisdiction).

[8] The political importance of Kupang increased greatly in 1749 when the Topasses were decisively defeated by the Dutch and their allies, which led to the extension of VOC influence over wide areas of western and central Timor.

Kupang was the final destination of William Bligh, who was set adrift in an open boat following the Mutiny on the Bounty (1789).

After travelling 3,618 nautical miles (6,710 km) from the Tonga Islands over 41 days, Bligh landed in Kupang on 14 June.

[9] News of his journey inspired a small party of nine convicts and two children to escape from the penal colony at Sydney Cove, Australia, they escaped from Port Jackson, Australia, and arrived at Kupang after ten weeks,[10] having travelled 3,254 nautical miles (6,026 km) in an open boat.

[11] VOC positions in the East Indies were attacked by British Forces following the occupation of the Netherlands by French revolutionary armies in 1795.

After the British occupation of Java, Kupang finally surrendered in January 1812, and the town was returned to the Dutch in 1816 following the end of the Napoleonic Wars.

[12] During his tenure, the Christian mission in the city experienced greater success than before, partially through the efforts of the missionary Reint LeBruyn (1799-1829).

Kupang's subsequent popularity with British and North American whalers was diminished by the late 19th century after the relocation of whaling areas, although the city was a free port after 1866.

The area around the city is geologically inactive, with soil composition characterised by non-volcanic materials such as Latosol and Terra rossa.

[17] The topography of the city is mostly low-lying but also includes groups of hills in the south and southwest, which has the effect of creating a relatively fertile catchment area.

This economic profile significantly differs from that of neighbouring regions, which still rely on agriculture and resource extraction as the primary contributor to their economies.

Industrial facilities in the city include three cement plants operated by PT Semen Kupang, which, in total, produce approximately 250,000 tons per year.

This gave rise to a plan by the provincial government to take over ownership of PT Semen Kupang in 2020 to increase production.

[36] As the capital of East Nusa Tenggara province, the city is also home to the provincial parliament building and the governor's office.

However, this was met with opposition from owners and drivers of local share taxi services, on the grounds that a BRT system would threaten their jobs.