Initially Frederikshavn was named Fladstrand meaning Flat beach due to its location in Flade parish. The first mention of a settlement, dated 13 March 1572, was found in the Danish chancery letterbooks. It was a fishing village, crossing point to Norway and trading place. Between 1686 and 1690 the old Fladstrand church was built.
During the Great Nordic War (1700-1721) the town saw a rise in activity as travelers to Norway embarked from here as the route through Sweden was cut. In 1733 a royal maritime pilot was stationed at the town after King Christian VI was forced to stay in the town due to bad weather on his journey to Norway.
Due to its advantageous proximity to the Baltic Sea, Frederikshavn has historically been a naval base of key importance. In 1627 under Kejserkrigen, Melchior von Hatzfeldt troops built a sconce north of the fishing village, known as Nordre Skanse. After the war it was manned by Danish troops. In 1675 the fortification was expanded with a sconce south of the harbor. In the period 1686-87 the fortification was expanded again with a heavy tower, a wall and a port. It was described as a citadel. The tower is known as Krudttårnet. In 1891 the wall and port were demolished, but the tower has been preserved. Today, the Krudttårnet is part of the coat-of-arms of the municipality. In 1735, fifty Danish men were stationed at the fortress. From the middle of the 18th century the military importance of the citadel was dwindling and some of the fortifications and buildings were disposed of. The citadel existed until 1864.
During the Gunboat War (1807-1814), the town saw increasing trade and activity. The first artificial harbor was constructed from 1808 to 1810.
Denmark’s downfall in the war had a great impact for Fladstrand. The military left and the town's largest source of income was gone. The general economic crisis in Denmark worsened the situation. The town did not have market town status, but trade, craft and other activities exclusive to market towns went on illegally in Fladstrand for several decades. The majority of the inhabitants had livelihoods based on crafts, services and trade, not production. This was used by the harbor directorate as an argument for giving Fladstrand market town status. On 25 September 1818 Frederik VI bestowed it a market town status under the name of Frederikshavn.