The first permanent settlement in the area of today's Wadowice was founded in late 10th century or early 11th century. According to a local legend, the town was founded by certain Wad or Wład, a short form for the Slavic name of Ladislaus. The town was first mentioned as Wadowicze in St. Peter penny register in years 1325–1327. In 1327 it is also mentioned (under the same name) in a fief registry sent from prince John I Scholastyk of Oświęcim to Bohemian king John I, Count of Luxemburg. At this time it was a trading settlement belonging to the Dukes of Silesia of the Piast Dynasty, and according to some historians it was already a municipality. In 1430 a great fire destroyed the town. It was soon rebuilt and granted city rights, along with a city charter and a self-government, based on the then-popular Kulm law. The privileges, granted by Prince Kazimierz I of Oświęcim led to a period of fast reconstruction and growth.
The administrative division of the region in the times of regional division was complicated. Initially, between 1313/1317 and 1445, Wadowice belonged to the Silesian Duchy of Oświęcim and after 1445 to the Duchy of Zator. In 1482 Władysław I of Zator inherited only half of his father's lands and created a separate Duchy of Wadowice, which lasted until his death in 1493. The following year his brother and successor, Jan V of Zator abdicated. At the same time the land was subject to Bohemian overlordship, which lasted until the following year, when the Duchy was bought by the Kings of Poland and incorporated as a Silesian County. Finally, the County was incorporated into the Kraków Voivodeship in 1564.
In the 16th-17th centuries Wadowice was a regional centre of crafts and trade. Among the most notable sons of the town was Marcin Wadowita, a theologian, philosopher and a deacon of the Kraków Academy. He was also the founder of a hospital and a basic school in Wadowice. However, several plagues and fires halted the prosperity and the town's growth was eventually halted as well.
In the effect of the 1st Partition of Poland, Wadowice was annexed by Austria and incorporated into the newly-established Kingdom of Galicia, under direct Austrian rule. The town's growth started soon afterwards, after a road linking Vienna with Lwów was built. The town became a seat of a communal administration and since 1867 - a county site. Small industries were developing slowly during the 19th century. New inhabitants settled in the area, attracted by the industry, new military barracks and various administrative institutions. In addition, a new hospital and a regional court were erected in the town centre. Finally, in the last 25 years of the 19th century partial liberalisation of the Austro-Hungarian monarchy led to creation of various Polish cultural and scientific societies.
After the World War I and the dissolution of the monarchy, Wadowice became part of the newly-reborn Poland. The seat of a powiat remained in the town and in 1919 the inhabitants of the area formed the 12th Infantry Regiment that took part in the Polish-Bolshevik War of 1919–1920. In 1920 Karol Wojtyła was born in Wadowice (later known as the bishop of Kraków and Pope John Paul II).
After the Polish Defensive War of 1939, Germany occupied the area and on October 26 Wadowice was annexed by Nazi Germany. On December 29 of the same year the town was renamed to Frauenstadt. Initially the Polish intelligentsia was targeted by harsh German racial and cultural policies and hundreds of people from the area, most notably priests, teachers and artists, were murdered in mass executions. Hundreds more were expelled and resettled to the General Government in order to make place for German settlers. Between 1941 and 1943 a ghetto was established in the city. Almost the entire local Jewish population (more than 2,000) was exterminated, mostly in the nearby Auschwitz concentration camp. In addition, the Germans set up a POW camp for Allied soldiers and a penal camp that served as a transfer camp for various German concentration camps. Despite German terror, the Home Army units were active in the area, most notably in the town itself and in the Beskid mountains to the south of it.
After the war, in 1945 Wadowice retained its powiat town status and until 1975 served as a notable centre of commerce and transport in the Kraków Voivodeship. After that the town was transferred to the newly-created Bielsko-Biała Voivodeship. After the peaceful transformation of the political and economical system in Poland (in 1989), most of the local industry was found inefficient and went bankrupt. However, the ecological and historical heritage of the area as well as its status as the birthplace of Pope John Paul II led to fast growth of tourism. Currently more than 200,000 people visit Wadowice every year and this number is rising.
Wadowice is today mainly a centre for tourism and sightseeing, but also a place for small industries such as the production of machines and construction materials. There is also the headquarters of the biggest juice-maker of Poland - Maspex - and the shoe producer - Badura.