Suwałki in its present state is located in the territories occupied in the Middle Ages by the Baltic tribes of Yotvingians. Later, these territories were part of the Grand Duchy of Lithuania and in 1386 became part of Poland. In 1667, by the priviledge granted by king Jan II Kazimierz, these territories came into the possession of the Hungarian Camaldolese. Towards the end of the 1690s, in the valley of the Czarna Hańcza River, at the trade route between Grodno and Królewiec, they established a village named Suwałki, which in 1720 received municipal rights from king August II Mocny. The well-off town, with a priviledge for organizing markets and fairs, was quickly developing as the local trade centre. Although the Camaldolese set a separate street for Jews and they encouraged them to settle there, at the beginning of the 18th century Suwałki was inhabited predominantly by Catholics stemming from northern Masovia.

As a result of the third partition of Poland, in 1796 the town became part of a new province – New East Prussia and after the Camaldolese Order in Wigry was annulled and its property confiscated Suwałki was taken over by the Prussian treasury. At the end of the 18th century, the town subjected to Prussia gained the status of an important legal and administrative, as well as trade and service centre. After the French-Prussian war (1806–1807) Suwałki lost its significance only to regain it after the establishment of the Kingdom of Poland in 1815 and the location of the province authorities in the town, and to develop economically as well as demographically. The next five decades brought an increase in the number of Suwałki's inhabitants nearly twentyfold, so that in 1872 Suwałki was the fourth biggest town in the Kingdom of Poland (after Warsaw, Łódź and Lublin). From the 19th century on, the town started to attract Jewish settlers on a large scale. In 1841 Jews accounted for more than half of the town's inhabitants and in the last quarter of the 19th century – over 60 per cent. In the 19th century and at the beginning of the 20th century a significant ethnic and religious group were the Orthodox Russians, mainly the tsar's clerks, who even before the First World War accounted for 6.7% of the town’s population. Another religious group among the Suwałki's inhabitants, which accounted for less than 6% of the whole population at the beginning of the 20th century, were protestants –Germans, Mazurians and Poles. On the eve of the 20th century, Suwałki’s population was enriched by a group of about 400 Lithuanians.

During the 19th century, the town underwent a radical redevelopment as designed by Karol Majerski. Many public (among others: two hospitals, a middle school and an abattoir) and sacral (among others: a new Catholic church, an Orthodox church and an Evangelical church) buildings were erected at that point in time. The roads were adjusted, a park substituted the former marketplace, a separate barracks district was established, and a new cemetery was set beyond the town's borders. At the end of the 19th century a new railway line from Petersburg to Warsaw crossed through Suwałki.

On the restoration of independence and the creation of the Second Republic of Poland, Suwałki, together with the whole Suwałki Region, were the subject of a dispute between Poland and Lithuania, which manifested itself, among others, with the Sejny Uprising (August 1919) and the occupation of Suwałki by Lithuanians during the Polish-Bolshevik War (July 1920). During the interwar period when Suwałki was a county town in the Białostockie Province, it was also a multi-ethnical and multi-religious centre inhabited by Poles, Jews, Germans, Russians, Ukrainians, and Byelorussians. The town was predominantly a trade centre with a relatively weakly developed industry and craftsmanship, plus a major cultural and educational centre, and one of the biggest garrisons in the Second Republic of Poland. In addition to national and private general schools, there were three middle schools, two teacher's seminars, a trade school, a merchant middle school, a vocational school, and a private music school. There were three cinemas, several libraries, choirs and amateur theatrical and literary groups. Printing houses in Suwałki published a dozen or so daily papers and periodicals, among others: "Ziemia Suwalska" (“The Suwałki Region”) and "Tygodnik Suwalski" ("The Suwałki Weekly”).

After the outbreak of the Second World War, on 24 September 1939, the Soviet army occupied Suwałki. As a result of the second Ribbentrop – Mołotow pact of 28 September, Suwałki and the part of the Suwałki Region were incorporated to the German Reich and became part of the eastern Prussian Gumbinnen (Gąbin) administrative region as Kreis Sudauen. Within days of the German army’s invasion of Suwałki, all Jews were expelled from the town and the neighbouring places, and the territory of the old kehilla (the so-called "Małe Raczki") was converted into a district for German officials. In the summer of 1941, the Germans established a camp for Soviet captives, in which some 30,000 – 46,000 people perished.

The town was liberated by the Soviet army in October 1944 after difficult and long-lasting fights, in consequence of which Suwałki suffered considerable damage. Although in the 1960s and 1970s several modern industrial plants ("Kolbet" Pre-Tensioned Ground Coats Factory, The Chipboards Factory, "Warmia" Clothing Industry Factory, and the aggregate mine in Sobolew) functioned there, Suwałki did not regain its former significance. The creation of the Suwałki Province with the capital in Suwałki in 1975 contributed to the town's development, but the political changes, which marked the year 1989, had a negative effect on the economy of Suwałki. After the administrative reform in 1999 and the liquidation of the Suwałki Province, Suwałki became one of the county towns in the newly created Podlaskie Province.