The castle was built by the Teutonic Order after the conquest of Old Prussia. Its main purpose was to strengthen their own control of the area following the Order's 1274 suppression of the Great Prussian Uprising of the Baltic tribes. No contemporary documents survive relating to its construction, so instead the castle's phases have been worked out through the study of architecture and the Order's administrative records and later histories. The work lasted until around 1300, under the auspices of Commander Heinrich von Wilnowe. The castle is located on the southeastern bank of the river Nogat. It was named Marienburg after Mary, patron saint of the religious Order. The Order had been created in Acre (present-day Israel). When this last stronghold of the Crusades fell to Muslim Arabs, the Order moved its headquarters to Venice before arriving in Prussia.

Malbork became more important in the aftermath of the Teutonic Knights' conquest of Gdańsk (Danzig) and Eastern Pomerania in 1308. The Order's administrative centre was moved to Marienburg from Elbing (now Elbląg). The Grand Master of the Teutonic Knights, Siegfried von Feuchtwangen, who arrived in Marienburg from Venice, undertook the next phase of the fortress' construction. In 1309, in the wake of the papal persecution of the Knights Templar and the Teutonic takeover of Danzig, Feuchtwangen relocated his headquarters to the Prussian part of the Order's monastic state. He chose the site of Marienburg conveniently located on the Nogat in the Vistula Delta. As with most cities of the time, the new centre was dependent on water for transportation.

The castle was expanded several times to house the growing number of Knights. Soon, it became the largest fortified Gothic building in Europe, on a nearly 21-hectare (52-acre) site. The castle has several subdivisions and numerous layers of defensive walls. It consists of three separate castles – the High, Middle and Lower Castles, separated by multiple dry moats and towers. The castle once housed approximately 3,000 "brothers in arms". The outermost castle walls enclose 21 ha (52 acres), four times the enclosed area of Windsor Castle. The developed part of the property designated as a World Heritage Site is 18.038 ha (44.57 acres).

The favourable position of the castle on the river Nogat allowed easy access by barges and trading ships arriving from the Vistula and the Baltic Sea. During their governance, the Teutonic Knights collected river tolls from passing ships, as did other castles along the rivers. They controlled a monopoly on the trade of amber. When the city became a member of the Hanseatic League, many Hanseatic meetings were held there.

In 1361, the future Grand Duke of Lithuania Kęstutis was briefly imprisoned in the castle. In 1365, Polish King Casimir III the Great visited the castle. In the summer of 1410, the castle was besieged following the Order's defeat by the armies of Władysław II Jagiełło and Vytautas the Great (Witold) at the Battle of Grunwald. Heinrich von Plauen successfully led the defence in the Siege of Marienburg (1410), during which the city outside was razed.

In 1456, during the Thirteen Years' War, the Order – facing opposition from its cities for raising taxes to pay ransoms for expenses associated with its wars against Kingdom of Poland – could no longer manage financially. Meanwhile, Polish General Stibor de Poniec of Ostoja raised funds from Danzig for a new campaign against them. Learning that the Order's Bohemian mercenaries had not been paid, Stibor convinced them to leave. He reimbursed them with money raised in Danzig. Following the departure of the mercenaries, King Casimir IV Jagiellon entered the castle in triumph in 1457, and in May, granted Danzig several privileges in gratitude for the town's assistance and involvement in the Thirteen Years' War (1454–66) as well as for the funds collected for the mercenaries that left. The mayor of the town around the castle, Bartholomäus Blume, resisted the Polish forces for three more years, but the Poles captured and sentenced him to death in 1460. A monument to Blume was erected in 1864.

Residence of the Polish kings

In 1466 both castle and town became part of the Polish Malbork Voivodeship in the province of Royal Prussia. Since 1457 it served as one of the several Polish royal residences, fulfilling this function for over 300 years until the First Partition of Poland in 1772. During this period the Tall Castle served as the castle's supply storehouse, while the Great Refectory was a place for balls, feasts, and other royal events.[5] Polish Kings often stayed in the castle, especially when travelling to the nearby city of Gdańsk/Danzig. Local Polish officials resided in the castle. From 1568 the castle housed the Polish Admiralty (Komisja Morska) and in 1584 one of the Polish Royal Mints was established here. Also, the largest arsenal of the Polish–Lithuanian Commonwealth was located in the castle. By the decision of King John II Casimir Vasa of 1652, Jesuits took care of the castle chapels of Mary and St. Anne.

During the Thirty Years' War, in 1626 and 1629 Swedish forces occupied the castle. They invaded and occupied it again from 1656 to 1660 during the Deluge.[18] Then the castle was visited by Swedish kings Gustav Adolf (in 1626) and Charles X Gustav (in 1656).

After the Partitions of Poland

After Prussia and the Russian Empire made the First Partition of Poland in 1772, the town was annexed by the Kingdom of Prussia and in 1773 it became part of the newly established province of West Prussia. At that time, the king's officers used the rather neglected castle as a barracks for the Prussian Army and also as a poorhouse. The last Jesuits left the castle in 1780. In 1794 David Gilly, a Prussian architect and head of the Royal Office of Works, made a structural survey of the castle, to recommend on its future use or demolition.[19] Gilly's son, Friedrich Gilly, produced several engravings of the castle and its architecture, which he exhibited in Berlin. These were published by Friedrich Frick between 1799 and 1803 and led the Prussian public to "rediscover" the castle and the history of the Teutonic Knights.[20]

Johann Dominicus Fiorillo published another edition of the engravings on 12 February 1803, also wanting to encourage public interest. Max von Schenkendorf was critical of the defacing of the castle. Throughout the Napoleonic Wars, the Prussian army used the castle as a hospital and arsenal. Napoleon visited the castle in 1807 and 1812. After the War of the Sixth Coalition, the castle became a symbol of Prussian history and national consciousness. In 1816, Theodor von Schön, governor of West Prussia, began the restoration of the castle. In 1910, the Naval Academy Mürwik in Flensburg was built, and the Marienburg was used as a model for this new Red Castle. The restoration of the Marienburg was undertaken in stages until the beginning of the Second World War.

With the rise of Adolf Hitler to power in the early 1930s, the Nazis used the castle as a destination for annual pilgrimages of both the Hitler Youth and the League of German Girls. The Teutonic Castle at Marienburg served as a blueprint for the Order Castles of the Third Reich built under Hitler's reign. In 1945 during fighting in the area, more than half the castle was destroyed.

In memory of the town's residents voting in favor of remaining part of Germany, after the First World War, a monument of a knight on a tall column was erected in front of the castle. The town was transferred to Poland in 1945, and most of its inhabitants fled or were expelled. In the course of Polonization, the column was cut in half. The upper part remains at the original location and now carries a statue of Mary, mother of Jesus, while the rest of the column can be found supporting a Saint Christopher statue in a monastery garden near St. John's church.