This area of North Carolina's Crystal Coast was originally known as Shepherds Point, describing the peninsula of land at the intersection of the Newport River and Beaufort Inlet. Planning for the development of this area was done by John Motley Morehead, NC governor from 1841 to 1845. His vision of 'a great commercial city' included extending the North Carolina Railroad from Goldsboro to Shepherd's Point.

Public sale of lots in the development area began in 1857. The railroad arrived in 1857. Further development was halted by The Civil War. The vision of Morehead City as an extensive port did not pan out in the years after the civil war ended, but the railroad allowed the local fishermen to provide fresh seafood to markets which had been too distant to reach before. A damaging storm in 1876 further hampered the development of the Morehead City port. It would be years before the port expanded from the pier and warehouse facility known as Pier #1. In the years after Pier #1 was installed, it handled mostly naval stores and salt.

In the early 1880s a replacement of the old Atlantic Hotel that had been destroyed by a hurricane was built. The Atlantic Hotel had 233 rooms and claimed to have the largest ballroom in the South. It drew the cream of the state's society to the coast until it was destroyed by fire in 1933.

A large section of the shore of the Newport river on the north side of Morehead City was settled by persons displaced from whaling communities on Shackleford Banks destroyed by the great hurricane of 1899.

Residents of Carteret County requiring medical attention in the early 1900's arrived by a variety of means to the doors of Dr. Ben F. Royal, Surgeon and Dr. William E. Headon, General Practitioner, who established the first hospital, Morehead City Hospital with seven beds on the second floor of a building in downtown Morehead. 1918 Dr. Royal raised $77,000 to build a 28 bed hospital on Morehead City 's waterfront. A dock received the many patients arriving by boat. The dock entrance was said to be often as busy as today's emergency room entrance.

The 1920's brought the growth of Crab Point, a part of the city east of Country Club Road and north of the 20th Street Bridge over Calico Creek. The area is named Crab Point because when tides came in crabs were trapped on the shoreline, making them an easy catch. In the early days Crab Point served as a port and had windmills for grinding grain and generating power for lumber companies.

Commercial fishing remained the primary endeavor for many Morehead City families. The railrod and the advent of refrigeration brought more distant markets within range of coastal fishermen. Primary species harvested included trout, flounder, drum, oysters, scallops, clams, menhaden, and mullet. On July 30, 1967, for a total cost of $2,137,417.74, the current facility Carteret General Hospital opened with 13 physicians and 177 employees. It was about this time that development began in many areas previously undeveloped throughout Carteret County. This development continued through the end of the century.

Currently, Morehead City is a major port for phosphate products. It can handle shipping containers using its larger cranes. Future plans include expansion onto property owned by the Ports Authority on Radio Island .

In recent years, a large charter-fishing fleet has developed. The town has regained its commercial viability as a modern port terminal as well as a being the 'sound-side' of the Atlantic Beach resort trade. The waterfront area has been revitalized, and restoration of the historic train station is underway. Land and property values have increased steadily as the area continues to be 'discovered' in our ever smaller world.