Long before Europeans settled here, many historic American Indian groups, as well as their ancient forefathers, called what is now Wayne County home. These tribes included the Shawnee, Chippewa, Ojibwa, Lenape (Delaware), Wyandot, Eel River, Kaskaskia, Haudenosaunee, the Munsee Tribe, Seneca-Cayuga, Ottawa, and Piankashaw.

The Treaty of Greenville designated the land that is now Wayne County, Ohio, as Indian Territory (1795). The Northwest Territory government authorized the formation of Wayne County in 1796, encompassing what would later become northern Ohio, as well as much of the lower and upper peninsulas of Michigan. Wayne County was incorporated into Michigan Territory when Ohio was formed in 1803, and later became Wayne County, Michigan. The current boundaries of Wayne County, Ohio, were established in 1808, but the county government was not established by the State of Ohio until 1812.

Some of the county's first residents were members of the Amish Christian religious group. The Amish community in Wayne County has grown to be one of the largest in the country. Many of the other early settlers were of German descent. August Imgard, a Wayne County resident, is credited with putting up the first Christmas tree in Ohio in 1847.

The county was named after General "Mad" Anthony Wayne, who won the Battle of Fallen Timbers in 1794. Residents named the county in honor of General Anthony Wayne, the victor at the Battle of Fallen Timbers in 1794.