The city of Eksj� most likely appeared sometime in the medieval ages when it was the centre for the thing, a regional council. It�s first mentioned is from the 14th century. It was given its charter in the early 15th century by the King Erik av Pommern.
In the 16th century Eksj� was one of the six Swedish cities in the province of Sm�land. The others were J�nk�ping, Kalmar,Vimmerby, V�stervik, and the seat of the diocese: V�xj�.
After the crowning of King Gustav Vasa in the 1524, the partisan leader Nils Dacke led a rebellion. Dacke took control of the area and was supported by the locals, also in Eksj�. After Dacke had been killed by the Royal army, his body parts were hung in public places, as to quench any notions of new uprising. Eksj� was one of the towns were body parts of Dacke were on public display. This may also have contributed to the decision of Gustav Vasa to revoke the city charter of Eksj� in 1544. There are several monuments and folk museums honoring these times around the province and in Eksj� municipality, and in the dense Sm�landian forests where Dacke lived.
During the Nordic Seven Years' War Eksj� was burnt to the ground in 1568 and subsequently rebuilt at a somewhat different location. The construction was led by the Dutch Arendt de Roy
