The city is at the mouth of the Cheboygan River on Lake Huron. US 23 connects with I-75 at Mackinaw City and the Mackinac Bridge, about 15 miles to the northwest. Rogers City is about 41 miles to the southeast. M-27 runs south from the city along the north shore of Mullett Lake to I-75 at Indian River about 18 miles to the southwest. M-33 runs due south along the east shore of Lake Mullett to M-68 about 20 miles to the south.

According to the United States Census Bureau, the Northern Michigan city has a total area of 7.0 square miles (18.1 km²), of which, 6.8 square miles (17.6 km²) of it is land and 0.2 square miles (0.5 km²) of it (2.72%) is water.