The Eyak people long had a village on the shore of Lake Eyak, located at the north end of today's Cordova. They were the brokers for trade between the Ahtna Athapaskans, Tlingit, and Alutiiq who came to the mouth of the Copper River. The Russians opened a post nearby in the 1790s, hoping to engage in the trade and expecting the post to be the base from which they would access interior Alaska following the Copper River. They were unsuccessful at achieving either aim.

The abundant salmon in the Copper River delta attracted two California companies to open canneries at Odiak Slough in the mid-1880s. The town of Cordova was created when Michael Heney started construction of a railroad paralleling the Copper River to the interior in 1906. Cordova had a deep water port. The railroad went 196-miles to the incredibly rich Kennecott copper mines in the Wrangell Mountains. During the railroad's years of operation, 1911-1938, over $200 million in copper ore shipped from Cordova.

The town was founded during America's Progressive Era, and much of the land around Cordova became part of Chugach National Forest when it was created in 1909. The forest was created, in part, to curtail the practice of consolidating individual mining claims to benefit large corporations and create monopolies. The Ballinger-Pinchot controversy, today a textbook example, was over consolidating claims in the Bering River coal fields outside Cordova.

Cordova was one of the major southcentral Alaska towns in the 1920s and 1930s. It had one of the first movie theaters, a number of fraternal organizations, and a federal building. The town became home base for a number of Alaska aviators who flew supplies that were brought to Cordova by ship to remote mines. After the railroad stopped operating in 1938, fishing became the town's economic base. Cordova was not far from the epicenter of the 1964 earthquake, and suffered major damage. Recovery was slow.

The market change from canned to frozen salmon proved to be a great opportunity for Cordova. Adept promotion of the early run of Copper River red salmon helped Cordova. The rebound was set back with the Exxon Valdez oil spill in 1989, but 25 years later fishing is flourishing. The Eyak and Alutiiq residents in Cordova used oil spill settlement funds to establish the Ilanka Cultural Center, one of the first in the state. Cordova is popular with fishermen, birders, and hunters.