The name of Chojnice comes from choina (plural: chojny), the name of a common coniferous tree typical of the forest surrounding the town. The spelling over the ages changed as follows: Choinicia, Honitcze, Choynicze, Chonecia, Conicia, Conecium, Konazia, Konnitz, Kunitz, Conic, Konitz. The town's coat of arms is also tied to the forest, as it bears the image of an ox head adorned with a flower between the horns.

Based on archaeological surveys, it can be said that at the turn of 11th and 12th centuries, this was the site of a settlement protected by a wood-and-earthworks wall. The first source mention of the settlement comes from 1275 and deals with the marking out of the boundaries of a holding of the Order of St. Augustine in the village of Swornegacie on behalf of Mestwin II, Duke of Pomerania, who was assisted by the monk Myśliboj Malowy of Chojnice. The settlement at the time was developing well thanks to a fortunate location at a crossroads of trade routes, among them one from Russia to Pomerania. In 1309, the whole of West Pomerania, Chojnice included, was taken over by the Teutonic Order.

Chojnice had its town charter renewed in 1326 and 1360. In the administrative and military sense, it was part of the Człuchów Province. The Teutonic Knights took advantage of Chojnice's natural defensible position (surrounded as it was by two lakes: Zakonne and Zielone) and constructed a system of fortifications comprised of earthworks, moats, and mighty defensive walls reinforced with 24 towers. Entry to the city was guarded by three gates. The well-fortified town was a vital element of the Teutonic Order's defences, earning it the name of the Pomerania's Gate. The Teutonic Knights also set about organising the town's development, the traces of which can still be seen in the regular layout of the old town. 

During the war between the Kingdom of Poland and the Teutonic Order in 1409-1411, Chojnice changed hands several times, but ultimately remained with the Order. In 1433, the city was ineffectively besieged by mercenary Hussite troops in Polish service. In 1440, Chojnice joined the Prussian Confederation. During the Thirteen Years' War (1454-1466) Polish troops again laid siege to Chojnice for several months to no effect. [[refr:] J. Knopek, B. Kuffel, Bitwa pod Chojnicami 18 IX 1454 r. w tradycji historycznej i regionalnej, Chojnice 2004.]] In the end, the town came under Polish rule in 1466 after the signing of the Second Peace of Thorn. That is when Gdańsk Pomerania and Chojnice returned to Poland after 157 years and became part of Royal Prussia.

Chojnice truly flourished in the 16th century, basing its prosperity on a well-developed textile industry. The town was also a centre of the grain trade. As early as the end of the 15th century, the town boasted a town hall. In 1555, the town council officially adopted the Lutheran faith, as did most of the townsfolk. After 60 years, the Catholics got back their gothic parish church, while the Evangelicals soon built their own church next to the town hall. On the initiative of the priest Jan Doręgowski, the Jesuits came to Chojnice and began missionary and educational work in a school (later a college) established in 1623. The Jesuits also built a baroque church in the 18th century (presently the Church of the Most Holy Annunciation) and a school building that stands to this day.

This period of prosperity came to an end with the Swedish invasion (1655-1660), when Swedish troops caused significant damage to the town. [[refr:] A. Kersten, Stefan Czarniecki 1599-1665, Warszawa 1963, 316-317.]] Worse still, the year of the invasion also saw a large fire break out in Chojnice, as well as a disease outbreak brought about by the invading troops, killing nearly 80% of the town's population. Further disasters befell the town during the Great Northern War (1700-1721). Over the course of the war the town was burned by Russian troops in 1707, and a cholera outbreak in 1711 killed roughly 1,000 inhabitants. Even more misfortune hit the town in 1733-1742, when the city was again afflicted by fires. After all that, Chojnice was rebuilt from the ruins over a period of thirty years. A number of houses built in the second half of the 18th century still stand to this day.

In 1772, as a result of the first Partition of Poland, Chojnice became a part of the Kingdom of Prussia under the German name Konitz. The town became the capital of the newly formed Chojnicki county. However, the town lost its autonomy in the process, and the new political situation caused a far-reaching social and economic regression. It was not overcome until the latter half of the 19th century. The main factors for the change were the construction of new roads to Nakło, Tuchola, and Kościerzyny (1856), the opening of a town gasworks (1870), and the starting up of rail transit on the Piła-Chojnice line, which was later extended to Tczew (1871-1873). Another railway line opened in 1877 to Szczecinek, another in 1894 to Nakło, and one in 1902 to Kościerzyna. 1900 also saw the activation of a waterworks and power plant, and a sanitary sewage system was established in 1909.

Following the Treaty of Versailles, Chojnicki county became part of the newly independent Second Polish Republic. An important road and rail transit route ran through Chojnice from Germany proper to Eastern Prussia. During the interwar period, the town served as the centre of administration, social life, education, culture, and tourism, becoming a hub of trade and services for the region of  Southern Kashubia and Tuchola Forest.

On September 1st 1939, German troops entered the city. During the occupation, the Germans persecuted and murdered the Poles and the remaining Jewish population. The main site for this was the so-called Death Valley (Polish: Dolina Śmierci), an area located in Pola Igielskie, where the invaders shot about 2,000 inhabitants from Chojnice and its surroundings. The remains of those murdered there were buried in the latter half of 1946 in the Cmentarz Ofiar Hitlerowskich cemetery at Gdańska street in Chojnice. [[refr.] B. Bojarska, Eksterminacja inteligencji polskiej na Pomorzu Gdańskim (wrzesień-grudzień 1939), Poznań 1972.]] During the war, the town and its surroundings organised underground education services and social aid, as well as a resistance group called Tajna Organizacja Wojskowa "Gryf Pomorski" (TOW "Gryf Pomorski"), which operated mainly in the forests of Chojnicki county. On February 14th 1945, Chojnice was taken by the Red Army. The town was returned to Poland. The fighting had destroyed 45% of the city structure, but rebuilding started immediately after liberation. Its first stage ended in 1950 with the renovation of the courthouse and post office.