Archeological findings testify that people lived in the vicinity of Anyksciai in the late Neolithic and the Bronze age. During the wars with Knights of the Sword these vicinities had an important defensive function. It's even suggested that on a large Seimyniskeliai mound some two kilometers to the North from the city which dates back to the X-XIII century there once stood Mindaugas capital Voruta. Recently, this view is being criticized. The mound had been arranged between the two 100-150 meter lowlands, where dammed creeks, Vorelis and Volupis, ran.
The settlement near the former mound Seiminiskeliai did not survive. After the wars with the Knights of the Sword were over, the new settlement was formed in a current location of Anyksciai. Hence, the basis for the two hypotheses of the city genesis.
In the location of the present day Anyksciai there was a settlement since very old times, because it was very convenient not only for living, but also for commerce. On the river Sventoji and then Neris and Nemunas goods were ferried to the Western parts of the country and the sea. It's possible, that even at the early one thousands there was a commerce road going from Vilnius to Riga. It was mentioned in 1338, and in the XVI century it was named "the great highway." Archeological findings illustrate the fact that back in the X-XII century merchants crossing Anyksciai vicinities had connections with the Russian cities. However, because of frequent assaults from Knights of the Sword Anyksciai settlement vanished early. It was reestablished only after Pabaiskas battle. This is the reason it has been mentioned in the written chronicles only after this time.
For now, it is known that in the authentic chronicles Anyksciai was first mentioned in 1442, i.e. seven years after Pabaiskas battle.
Anyksciai was a property of the lord (or his representative) and of a rector of the church (his was a smaller part). There were disagreements between them in 1529, 1530, 1538, 1540 and later with frequently changing priests as well as the lords. This had a detrimental effect on the city.
Maybe, the first time Anyksciai was marked on the map it was on 1578-1580 M. Strubicius map, which depicts arena of the war between Lithuanian-Polish Commonwealth (Rzeczpospolita) and Russia. The city was indicated only on the left side of the Sventoji.
In 1919 rural district (valscius) was created, in 1922 wool combing and spinning workshop was established, in1926 wine workshop was built. Back in 1916 Lithuanian grammar school was reestablished, and in 1920 a gymnasium. In 1922 a monastery and next to it a folk school were founded. Jewish elementary school that was created in 1910 was reestablished as well.
In 1938 Anyksciai was granted the city rights. At the time it, also, was a significant summerhouse location. Number of craftsmen had increased, more wine was being produced. However, the trade went down. Population before the WWII was about 4000.
Anyksciai was devastated during the years of fascist occupation. Many residents were executed, in 1944 both bridges were blown up, the city center and Uzupis jurisdiction was destroyed. City's economic activity was paralyzed.
Because Anyksciai was frequently devastated by fires, almost no valuable buildings remain to this day. The city's urbanistic value is determined by some unique features of its plan and spatial composition, and its unique urban development .