Brainerd is located just north of the geographical center of Minnesota, in a relatively hilly terminal moraine area created by the Superior Lobe of the Labradorian ice sheet. The town occupies land on both sides of the Mississippi River, though the older parts of Brainerd are almost all to the east.

Though the city itself has relatively few lakes, there are over 460 lakes within 25 miles (40 km) of Brainerd, located mostly to the north. For this reason, Crow Wing County and parts of the adjoining counties are often collectively referred to as the Brainerd Lakes Area.

According to the United States Census Bureau, the city has a total area of 8.4 square miles (21.9 km²), of which 8.0 square miles (20.6 km²) is land and 0.5 square miles (1.2 km²) (5.57%) is water.

Minnesota State Highways 18, 25, 210, and 371 are four of the main routes in the community.

Brainerd has been assigned ZIP code 56401 by the USPS.