The town was formed in 1829, as the construction of the Ohio and Erie Canal along the west bank of the Scioto River brought new growth to the area.

Historians believe that Waverly and the surrounding areas were inhabited by nomadic people as early as 13,000 BC.

There is evidence pointing to the emergence of the Hopewell culture in the Waverly area beginning about 300 BC.

Sometime after 1000 AD, the Fort Ancient people began to occupy southern Ohio, only to disappear in the 17th century, likely decimated by infectious diseases spread in epidemics from early European contact.

[4] It is not known whether the Shawnee were descendants of the Fort Ancient, but there are a number of similarities between the two cultures that have led some to speculate that this is the case.

There is also evidence to suggest that Siouan nations such as the Mosopelea may be descendants of the Fort Ancient culture.

One of the most well-known leaders of the Shawnee tribe, Tecumseh, was born somewhere very close to Waverly, perhaps just north of the city's site, in 1768.

As early as the age of 15, after the American Revolutionary War ended in 1783, Tecumseh was fighting alongside other Shawnee to stop the white invasion of their lands by attacking settlers' flatboats traveling down the Ohio River from Pennsylvania.

In time, Tecumseh came to lead his own band of warriors and his bravery and leadership have caused him to become an American folk hero and his legend still lives large in Waverly and the surrounding areas.

The initial plan for the Canal's route was likely not through Waverly, and it is believed that several noteworthy interested parties, including Robert Lucas and James Emmitt, had a hand in redirecting the route of the Canal to pass through or near their land, thereby benefiting them personally.

In the end, despite a number of reported irregularities in the special election, the Waverly supporters were victorious, and on November 11, 1861, the county commissioners ordered the removal of the county offices to Waverly pending the completion of suitable rooms to accommodate the move, which happened shortly thereafter.

James Emmitt was one of Waverly's most prominent inhabitants in the nineteenth century and was one of the wealthiest and most influential southern Ohioans of the time.

There has been some evidence linking Madison Hemings to Jefferson, but historians continue to debate the issue.

[9] During the Civil War years of 1861-1865, Waverly was impacted by the conflict; more than 100 Pike County residents died.

[10] In 1953, the Federal Government chose Pike County as the location for the Portsmouth Gaseous Diffusion Plant, designed to enrich uranium.

[10] During this time, government housing projects were undertaken, school facilities were expanded and improved, and many new businesses were started in Pike County.

[6] Historian James W. Loewen cites Waverly as a rare example of a town that barred blacks as early as the Civil War,[12] and asserts that the community was one of a number of Midwestern cities created for the purpose of excluding all races but whites.

[21] Waverly is the hometown of the Pure Prairie League, a pioneering band of the country rock genre.