The Museum of the Second World War in Gdansk was established on September 1st, 2008, through a regulation by the Minister of Culture and National Heritage. On the same day, Prime Minister Donald Tusk appointed Professor Paweł Machcewicz as the representative for the museum, and a team was formed to develop the concept for the museum's program. The team was comprised of historian Piotr M. Majewski from the Warsaw University and Janusz Marszalec, who previously served as the head of the Public Education Department at the Institute of National Remembrance in Gdańsk.
The concept for the museum was presented to the public on October 6th, 2008, during a discussion with historians and museologists at the Chancellery of the President of the Council of Ministers in Warsaw. The concept and record of the discussion were published in print and are accessible through the museum's website. The development of the concept and exhibitions was a collaboration between renowned scholars of World War II and totalitarianism, including Norman Davies, Timothy Snyder, Tomasz Szarota, Włodzimierz Borodziej, and Jerzy Wojciech Borejsza.
On November 26th, 2008, the Minister of Culture and National Heritage, Mr. Bogdan Zdrojewski, changed the name of the institution from the Westerplatte Museum to the Museum of the Second World War in Gdansk. He also defined the scope of the museum's operations as "amassing a collection related to the history of World War II, safeguarding it, and making it available to the public through exhibitions, popularization, education, and publishing".
The Minister of Culture and National Heritage, Mr. Piotr Gliński, announced on April 15, 2016 that the Museum of the Second World War and the Museum of Westerplatte and the War of 1939 would be combined. This decision was based on negative reviews written by Jan Żaryn, Piotr Semka, and Piotr Niwiński that were ordered by the ministry. However, in December 2016, the Voivodeship Administrative Court in Gdańsk questioned the decision to combine the museums and ordered a halt to the process until the case could be examined. The Ministry of Culture considered the court's decision to be invalid.
The Supreme Administrative Court overruled the Voivodeship Administrative Court's decision in January 2017. However, the Voivodeship administrative court in Warsaw halted the combination of the museums in January 2017 until a complaint filed by the museum's management and the Commissioner for Human Rights could be lawfully examined. Despite this, the museum was opened to the public on March 23, 2017. The Supreme Voivodeship Court eventually overruled the motion to suspend the regulation of the Minister of Culture and National Heritage on April 6, 2017. Dr. Karol Nawrocki was then appointed as the acting director of the combined facilities.
In September 2019, a statue of Witold Pilecki was erected in front of the museum. The statue depicts Captain Pilecki in his uniform and camp cap, and was designed by Mr. Maciej Jagodziński-Jagennmerr. The cost of the design, casting, and erection was PLN 400,000.
Poland's Prime Minister, Donald Tusk, launched an architectural competition to design the main building of the museum. The judging panel was made up of renowned experts, including Daniel Liebeskind and Jack Lohman, Director of the Museum of London. The winning design was created by Kwadrat architectural studio based in Gdynia. The museum is located on Wałowa Street, facing the Motława River, near the Radunia Canal and the historic Polish Post Office Building. It covers an area of 2.5 acres, with the building taking up 23,000 square meters. The building consists of three spheres symbolizing the connection between past, present, and future. Its most striking feature is a 40-meter tall leaning tower with a glass facade, housing a library, reading rooms, conference rooms, cafes, and restaurants with panoramic views of Gdańsk.