The earthworks rose in at least three construction stages over an estimated 400 years. The builders loosened soil with deer shoulder blades, split elk antlers, clamshell hoes, and digging sticks, then carried it in baskets holding 35 to 40 pounds to the growing walls. Archaeologist Patricia Essenpreis, who excavated the site from 1982 until her death in 1991, demonstrated that the embankment walls were built in multiple stages with post structures at their bases. Her colleague Robert Connolly continued the work through 2006, discovering that alternate basket loads of different soils were deliberately layered into the construction and that three-level limestone pavements lined the wall exteriors. One pavement contained a cache of burnt animal bones. In the North Fort interior, excavations revealed 10 habitation structures, evidence that people lived and worked within these walls as well as building them.

The defensive interpretation held for over a century after the Philadelphia Port Folio published the first map and description of Fort Ancient in 1809. Edwin Hamilton Davis and Ephraim George Squier, in their landmark 1848 work Ancient Monuments of the Mississippi Valley, called it 'one of the most extensive, if not the most extensive, work in the entire West.' But the evidence never quite fit. Eighty-four gateways are too many to defend. Ditches inside the walls serve no military purpose. No evidence of a large resident garrison has been found. The current interpretation, supported by decades of archaeological research, is that the walls served social, economic, political, and ceremonial functions. In the northeast corner of the complex, four circular stone-covered mounds arranged in a square mark the key discovery: the southwest mound aligns through gateway openings in the walls to track significant solar and lunar events.

The State of Ohio purchased the land in 1891, making Fort Ancient the state's first park. Warren K. Moorehead had conducted some of the initial excavations in 1887, publishing his findings in Fort Ancient: Great Prehistoric Warren County Ohio. The research never stopped. William C. Mills dug in 1908. Richard Morgan and Holmes Ellis worked from 1939 to 1940. Robert Riordan began excavations in the North Fort in 2006, revealing complex series of posts and activity areas with evidence of intense burning, and naming the Moorehead Circle after the pioneering archaeologist. The site was designated a National Historic Landmark, and in September 2023, it received UNESCO World Heritage status as part of the Hopewell Ceremonial Earthworks, alongside the earthworks at Hopewell Culture National Historical Park and the Newark Earthworks.

Long after the Hopewell builders departed, a culture that archaeologists named Fort Ancient lived near the complex, their name drawn from the place rather than the other way around. Centuries later still, a 19th-century American village grew on the eastern bank of the Little Miami River at the base of the earthworks, complete with a post office established in 1846, a hotel, a blacksmith shop, and other businesses. The village no longer exists. A stone building from 1802 that operated as the Crossed Keys Tavern from 1809 to 1820 remains on the river's west bank, listed on the National Register of Historic Places. Fort Ancient was once a stop on the Little Miami Railroad, and that former rail corridor now carries the Little Miami Bike Trail along the river.

The site's museum covers 1,500 years of American Indian heritage in the Ohio Valley, from North America's earliest inhabitants through the development of agriculture to the collision with European settlers. The earthworks themselves remain the primary draw: the wooded bluff rising above the Little Miami River, the undulating walls tracing their ancient pattern through the trees, the mounds aligned with celestial events that the builders tracked with a precision that still impresses astronomers. Fort Ancient is owned and operated by the Ohio History Connection and is open to the public Wednesday through Saturday from 10 AM to 5 PM and Sunday from noon to 5 PM. A canoe livery and private campground occupy the riverbank where the vanished village once stood.