Much of the area's earliest history is known from Captain William Clark's journal describing the January 1806 visit by a small expedition party from Lewis and Clark's Corps of Discovery. Clark's maps and journals describe a small village of several wood houses of the native Tillamook people who lived on both sides of the creek he named Ecola. The native inhabitants of the coast were becoming accustomed to visits from trading ships. For years, explorers and traders had been in contact with the native tribes.

In 1811, the first American settlement in the west, Fort Astoria, was established. The region grew as part of the American West and fortunes were made in fur trading and fishing. By the mid-1800s, the Native American population had dropped by 90 percent due to diseases introduced by explorers, traders and settlers.

As access to the region improved in the 1850s, logging grew to become the state's major industry and visitors and homesteaders began to make their way to the area. Visitors traveled by steamer down the Columbia, then by wagon roads to Seaside, where the first overnight lodging accommodations were established. Over the next 20 years, a few settlers made their way over Tillamook Head to homestead near Ecola Creek.

When railroad lines were finally finished between Astoria and Seaside in the late 1890s, homesteading expanded to this area, then known as Elk Creek. After the turn of the century, the area south of the creek was divided into small lots, which sold for $100 each.
Improvements on the road from Seaside continued and in 1911 a bridge was built over the creek. That year, Oregon governor Oswald West visited the area, staying at the Warren Hotel in Tolovana. West was the first guest at the new hotel and his name appears on the hotel register on display at the Cannon Beach History Center. West was also responsible for making the state's beaches public, passing legislation in 1913 declaring the shoreline a public highway. That year, West also built a large log home overlooking Haystack Rock. The original home was destroyed by fire in the 1990s, but was rebuilt at the same location. The log home can be seen from the beach just south of Haystack Rock.

In the 1930s, with the completion of Highway 101, the automobile replaced the train as the way to reach the coast. When Highway 26 was completed, Cannon Beach became a short drive from Portland.