Milton is located in the northern tip of Fulton County, encompassing 39.2 square miles of land. It is bordered by the city of Alpharetta to the east and south, Roswell to the south, Cherokee County to the north and west, and Forsyth County to the northeast.
The city's physical geography is characteristic of the Piedmont region of the Southeastern United States. The terrain is marked by rolling hills, expansive pastures, and dense forests of pine, oak, and hickory.
Several small creeks and streams wind through the city, feeding into the larger Chattahoochee River watershed. Because Milton has consciously restricted high-density commercial and residential development, much of its geography remains green, featuring conservation lands, large private farms, and scenic country byways that lack the heavy commercialization seen in neighboring municipalities.