Queensland's most extensive limestone belt lies near the township of Chillagoe, west of Cairns. In contrast with Australia's predominantly impounded karst settings, the limestones of the Chillagoe Formation occur as tower karst. Many of the limestone pinnacles are cavernous.

Local aboriginal groups have long known of the cave systems. Ceremonial and occupation sites have been recorded, most often associated with broad overhangs, rather than labyrinthine cave systems.

The first white explorer in the district was probably James Venture Mulligan in 1874, one year after his discovery of the Palmer River goldfield to the north. Mulligan and Harry Hammond further explored the Chillagoe region in 1883 on a trip down the Walsh River in search of copper. This and other prospecting trips in the mid 1880s were the precursors of mining development in the region.

Mining and pastoralism developed hand in hand, and William Atherton from Emerald end near Mareeba ventured west in 1887, and in the following year established Chillagoe Station by applying for 200 square miles of grazing country. A substantial timber homestead was built on the banks of Chillagoe Creek, on the outskirts of the present-day settlement.

William Atherton quickly became the first Chillagoe cave tour guide, escorting visitors to such localities as the Royal Arch and Donna caves, both of which are still maintained as guided tour caves.

Around the turn of that century, the tempo of mining and exploration had increased, the railway was making more country accessible, and many, many more caves became commonly known. It was not until the 1920s, however, that cave trusts were formed at both Chillagoe and nearby Mungana to manage the larger, better known caves in these areas. These cave trusts were partly funded by the two local authorities, and from fees received. With these funds, the trusts employed caretaker-guides, whose activities included the provision of rough infrastructure in the Spring, Geck and Cathedral caves at Mungana, and the Royal Arch and Fairy caves at Chillagoe. In this period, the majority of cave visitors to the area were transported by rail, though horse-drawn buggies were also popular.

With the decline in mining activity in the late 1920s and early 1930s, much of the population of the Chillagoe district drifted away, and the two local authorities were amalgamated into the present Mareeba Shire, and the cave trusts were abandoned.

In 1940, the Queensland Government gazetted National Parks over nine of the cave areas, totalling 1875 hectares and ranging in size from the Royal Arch National Park of 1514 hectares, to four national parks each less than one hectare. The design of the boundaries of these Parks, and their scattered locations, has been the cause of on-ground management problems to this day.

Although a rationalisation, amalgamation and re-gazettal in late 1998 has seen the declaration of the Chillagoe-Mungana Caves National Park of 3690 hectares, some Park areas remain small and isolated, largely due to continued interest in mineral resources on the surrounding lands.

Following the disbandment of the cave trusts, interested Chillagoe locals such as Paddy Byrne (of Byrne's Imperial Hotel, and local taxi driver) would guide visitors through the caves.

It was not until 1963 that the Department of Forestry, the body responsible for the administration of National Parks at that time, appointed Vince Kinnear as a part time guide. Vince was the local Postmaster and a keen and energetic speleologist, who maintained his interest in and love of the caves of Chillagoe through to his death in late 2000. In 1966 Vince's employment was elevated to a full-time capacity, and from then until 1978 he oversaw the management of the National Parks in the Chillagoe-Mungana area. This was a period of major expansion, with the construction of walking tracks through the Royal Arch and Ryan Imperial caves, and the design and construction of the walking tracks and lighting system in the Donna Cave. The Trezkinn cave, discovered in 1967 by Vince Kinnear and Frank Trezise, was fitted out with high-level walkways and a lighting system in the 1980s, and now joins the Donna and Royal Arch caves as one of the three guided cave tours offered daily.

The Queensland National Parks and Wildlife Service became a separate entity from the Forestry Department in 1975, and has maintained administration of the Parks and provision of cave tours since. There are currently five full-time Ranger-guides employed at Chillagoe. Their duties extend beyond their shared cave-guiding roster, to include broader land management activities as well as construction and maintenance of visitor facilities. Cave tours are offered every day except Christmas Day.