The present municipality known as Greater Napanee was created by amalgamating the old Town of Napanee with the townships of Adolphustown, North and South Fredericksburgh and Richmond in 1999.
The area was originally settled by Loyalists in the late 18th century and was first incorporated in 1854 . The original hamlet of Napanee is located at the site of a waterfall on the Napanee River, and was first known as Clarksville after Robert Clark, who built a grist mill here. Sir John A. Macdonald, Canada's first prime minister, who practiced law in Napanee, was said to have an affinity for the town, and today many surveys have said it to be one of the prettiest towns in the province.