The first written mention of Chełmno is known from a document allegedly issued in 1065 by Duke Bolesław II the Generous of Poland for the Benedictine monastery in Mogilno.

The town was made the nominal see of the Roman Catholic Diocese of Chełmno under the archbishop of Riga by the papal legate William of Modena in 1243 (however, the cathedral and the residence of the bishop were located actually in the adjacent Chełmża).

In 1440, the town was one of the founding members of the Prussian Confederation, which opposed Teutonic rule,[9] and upon the request of which King Casimir IV Jagiellon reincorporated the territory to the Kingdom of Poland in 1454.

[15] Also as part of anti-Polish policies, the Prussians expelled the Kraków professors from Chełmno,[11] abolished the local Polish academy, and closed down Catholic monasteries.

[17] On 22 January 1920 Polish troops were greeted by a large crowd of residents and Chełmno was reintegrated with Poland, which regained independence after World War I.

[18] The atrocities took place in Klamry, Małe Czyste, Podwiesk, Płutowo, Dąbrowa Chełmińska, and Wielkie Łunawy, while many other Poles were executed in forests.

The rest of the Polish population was expelled to the General Government in the more eastern part of German-occupied Poland in line with the German policy of Lebensraum.

Polish Secret State resistance groups such as Polska Żyje ("Poland Lives"), Rota, Grunwald, and Szare Szeregi were also active in the area.

On 25 January 1945 German forces set fire to several buildings in the city, including a hospital, a railway terminal, and a brewery, while retreating (see scorched earth).