Brown City was established in 1879 as a station on the Port Huron and Northwestern Railway, later a part of the Pere Marquette Railroad. The area quickly grew to become an efficient shipment point for lumber and grains. Brown City was incorporated as a village in 1887 and as a city in 1907. The "Marquette Flyer" provided early rail passenger and mail service between Detroit and Ludington. In the 1920s the Pere Marquette came under the control of the Chesapeake and Ohio Railway and was formally merged into it on 6 June 1947.