The exact origin of the town name is not known, but it is derived from the Lithuanian word vilkas (which means wolf).

[1] According to a legend, people who lived on the opposite side of Nemunas river heard the packs of wolves howling in the surroundings of the place where contemporary town is situated; since then, this land was called Vilkija and this name may have been derived from words vilkų gauja meaning a pack of wolves.

[citation needed] Names in other languages include Polish: Wilki; Yiddish: ווילקי, romanized: Vilki.

The land and water trade routes Vilnius-Königsberg passed through Vilkija, which encouraged the growth of the settlement.

During summer and fall 1941, mass executions of 800 Jews were perpetrated by an Einsatzgruppen of Germans and Lithuanian nationalists.