The town of Bremerhaven in Germany was founded in 1827, but neighboring settlements such as Lehe were in the vicinity as early as the 12th century, and Geestendorf was "mentioned in documents of the ninth century". These tiny villages were built on small islands in the swampy estuary. In 1381, the city of Bremen established de facto rule over the lower Weser stream, including Lehe, later therefore called Bremerlehe. Early in 1653, Swedish Bremen-Verden's troops captured Bremerlehe by force.

The Emperor Ferdinand III ordered his vassal Christina of Sweden, then Duchess regnant of Bremen-Verden, to restitute Bremerlehe to Bremen. However, Swedish Bremen-Verden began the First Bremian War (March – July 1654). In the subsequent peace treaty (First Stade Recess [de]; November 1654) Bremen had to cede Bremerlehe and its surroundings to Swedish Bremen-Verden. The latter developed plans to found a fortified town on the site, and much later this location became the present-day city of Bremerhaven. In 1672, under the reign of Charles XI of Sweden, in personal union Duke of Bremen-Verden—colonists tried unsuccessfully to erect a castle (named Carlsburg after Charles XI) there; this fortified structure was meant to protect, as well as control shipping heading for Bremen.

Finally, in 1827, the city of Bremen under Burgomaster Johann Smidt bought the territories at the mouth of the Weser from the Kingdom of Hanover. Bremen sought this territory to retain its share of Germany's overseas trade, which was threatened by the silting up of the Weser around the old inland port of Bremen. Bremerhaven (literally in English: Bremener Haven/Harbour) was founded to be a haven for Bremen's merchant marine, becoming the second harbour for Bremen, despite being 50 km (31 mi) downstream. Due to trade with, and emigration to North America, the port and the town grew quickly. In 1848, Bremerhaven became the home port of the German Confederation's Navy under Karl Rudolf Brommy.

The Kingdom of Hanover founded a rival town next to Bremerhaven and called it Geestemünde (1845). Both towns grew and established the three economic pillars of trade, shipbuilding and fishing. Following inter-state negotiations at different times, Bremerhaven's boundary was several times extended at the expense of Hanoverian territory. In 1924, Geestemünde and the neighbouring municipality of Lehe were united to become the new city of Wesermünde, and in 1939 Bremerhaven (apart from the overseas port) was removed from the jurisdiction of Bremen and made a part of Wesermünde, then a part of the Prussian Province of Hanover.

Bremerhaven was one of the important harbours of emigration in Europe.

As possibly the most critical North Sea base of the Kriegsmarine,  of the city was destroyed in the Allied air bombing of Bremen in World War II; however, key parts of the port were deliberately spared[citation needed] by the Allied forces to provide a usable harbour for supplying the Allies after the war. All of Wesermünde, including those parts which did not previously belong to Bremerhaven, was a postwar enclave run by the United States within the British zone of northern Germany. Most of the US military units and their personnel were assigned to the city's Carl Schurz Kaserne. One of the longest based US units at the Kaserne was a US military radio and TV station, an "Amerikanischer Soldatensender", AFN Bremerhaven, which broadcast for 48 years. In 1993, the Kaserne was vacated by the US military and returned to the German government.

In 1947 the city became part of the federal state Free Hanseatic City of Bremen and was consequently renamed from Wesermünde to Bremerhaven. Today, Bremerhaven is a city in its own right, but also part of the city-state of Bremen, which is for all intents and purposes a state comprising two cities. In addition to being part of the federal state, the city of Bremen has owned the "overseas port" within Bremerhaven since 1927. This and other parts of Bremerhaven owned by the city of Bremen are known as stadtbremisch. To complicate matters, a treaty between the two cities (as mentioned in Section 8 of Bremerhaven's municipal constitution) makes Bremerhaven responsible for the municipal administration of those parts owned directly by Bremen.