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Waverly is a city in Rock Creek Township in the northeast corner of Coffey County in east-central Kansas.

Waverly was founded and platted in 1878 by Isaac Pierson, the land's original owner and one of the area's first settlers, who named it for his hometown of Waverly, Indiana.

Waverly's first post office was established on June 10, 1878, with A. N. Sylvester as the first postmaster; Sylvester also opened the town's first store that same year.

The town grew up with the Ottawa & Burlington Railroad, completed through the site in 1878, and a Waverly town company was chartered in 1880.

By 1910 Waverly was the second-largest and most important town in Coffey County, standing at the junction of the Atchison, Topeka & Santa Fe and Missouri Pacific railroads as the most important shipping point between Burlington and Ottawa; its population peaked at 751 that year.

The 2020 census counted 574 people in Waverly, covering 0.73 square miles; in 2010 the city had 592 people in 229 households.

Waverly is the headquarters of Lebo–Waverly USD 243, a district of about 500 students that unusually maintains two separate small high schools — Waverly High School and Lebo High School — along with grade schools in both towns.

Waverly Junior-Senior High School, home of the Bulldogs, enrolls only about 94 students in grades 6–12, and its fiercest rivalry is with its own sister school, Lebo High School, in the Lyon County League.