[4] Founded in what was then known as Indian Territory, Waynoka was established in 1887 when the Southern Kansas Railroad, a subsidiary of the Atchison, Topeka and Santa Fe Railway, built a rail line through the area.

When the Cherokee Outlet opened up for non-Indian settlement in the land run of September 16, 1893, Waynoka became the area's agricultural trade center.

[5] The Santa Fe Railway made the city a major railroad center when it built Oklahoma's largest rail yard in Waynoka.

Ultimately employing a thousand machinists, boilermakers, sheet metal mechanics, fire builders, car men, switchmen, and engineers, it operated twenty-four hours a day.

In addition, a roundhouse, maintenance and repair shops, a reading room, a depot, and a Harvey House were built by the railroad.

At the turn of the twenty-first century, between fifty and one hundred trains still passed daily through Waynoka on Oklahoma's fastest and busiest rail line.

TAT offered passengers coast-to-coast travel in forty-eight hours,[5] and Waynoka was an important stop on the pioneering route.

[11] The current Waynoka Municipal Airport (FAA Identifier: 1K5) is one mile southeast of town, and features a paved 3532’ x 60’ runway.

Other NRHP-listed locations in town are the First Congregational Church at 1887 E. Cecil St., and the Waynoka Telephone Exchange Building at 200 S. Main St.