Versions of the city's name in other languages include Polish: Johaniszkiele, Russian: Иоганишкели Ioganishkeli, Yiddish: יאַנישקעל Yonishkel.

The Joniškėlis estate, which belonged to Karpis family in known from the 17th century.

In 1736 King of Poland and Grand Duke of Lithuania Augustus III granted rights to organize market in the town.

Before World War II, around 20% of the total population was Jewish.

[1] During the summer 1941, 200 Joniskelis Jews were shot to death by Germans in the Žadeikiai Forest in Pasvalys.