July 29, 1252 Curonian bishop and vice-regent of Livonian Order signed the agreement, that was approved by the ruler of Lithuania Mindaugas. Following this agreement Klaipeda castle was built. In the small port neighboring the castle, vessels of Lubeck and Bremen merchants used to moor.
In the middle of the 16th century Klaipeda's rivals, the inhabitants of Danzig, overloaded the Dane port with stones, therefore till 1820 only small vessels could enter the port.
In 1743 the first timber trade office was founded in Klaipeda. Klaipeda port was the most famous timber trading port Baltic – wide.
The chronicle of 1797 mentions that Klaipeda port consists of: the Dane river port and a big water basin in the strait of the Curonian Lagoon. Timber was handled in the port, accommodating more than 300 vessels at a time.
In 1919 when Germany lost the First World War, following Versal Agreement, Klaipeda port was transferred to Antante Alliance, and the Prime – Minister of France declared that “Klaipeda region has always been a Lithuanian one”.
June 27, 1923 a big meeting was held following the news that Klaipeda port was going to be transferred to Klaipeda town.
May 8, 1924 Klaipeda Convention was signed in Paris. Following this convention the management of Klaipeda port was passed to the port directorate, consisting of the representatives of the Lithuanian State, Klaipeda region and the Union of Nations.
1924-1939 was a period when Klaipeda port was at its flourishing peak – new quays were constructed, various companies started to operate, Lithuanian Shipping Company was founded. The state of Lithuania invested 42 million litas into the development.
In 1963 the first renewed Sea Festival took place. Today, the festival is becoming the most important Klaipeda’s mass event.
In 1986 the new International Ferry Terminal was constructed. The Terminal was constructed for serving the Soviet Army, located in Germany. The biggest rail ferries in the world began their operations.
In 1991, according to the Decree of the Government the Republic of Lithuania, the Ministry of Transport and Communications established State enterprise Lithuania Seaports Authority.
In 1991, Klaipėda Harbour Master’s Office, independent from Lithuania Seaports Authority was established.
In 1992, Klaipėda Port was granted the status of the State Seaport.
In 1993, according to the Decree of the Government of the Republic of Lithuania, State enterprise Lithuania Seaports Authority was renamed as State enterprise Klaipėda State Seaport Authority.
In 1993, Klaipėda Harbour Master’s Office and State enterprise Klaipėda State Seaport Authority were merged.
In 1996, Klaipėda State Seaport Act was adopted, whereby the port land, port waters, quays, hydrotechnical installations, shipping routes and channels, and other infrastructural facilities were declared the property of the state and not subject to privatization. These objects are controlled and developed by State enterprise Klaipėda State Seaport Authority.
In 2001, according to the Order of the Ministry of Transport and Communications, Maritime Safety Administration, an affiliate of Klaipėda State Seaport Authority was established.
In 2002, Maritime Safety Administration was separated from Klaipėda State Seaport Authority and the budgetary institution Lithuanian Maritime Safety Administration was established instead.