A wooden church was built here around 1200, replaced in the 1500s by a stone church, which was itself rebuilt to a larger size in 1666. The tower was added in 1784 and survives from that earlier building. By the 1880s the old church was considered unsatisfactory, and after decades of debate it was demolished in 1887. The present neoclassical church was built in 1887–89 to designs by the architect Johan Fredrik Åbom, incorporating the older tower, which was raised in height and given a new pointed spire.
The church consists of a nave with north and south transepts, the tower to the west housing the main entrance, and a five-sided sacristy extension to the east. Its barrel-vaulted ceiling was originally lined with tongue-and-groove panelling; stucco decoration designed by Allan Norblad was added during a 1912 renovation. A further renovation in 2000–2001 gave the interior its current light appearance, and the church's 1889 altar rail was uncovered and made movable, with a new consecration altar introduced.
Despite the rebuilding, Eksjö kyrka retains a good deal of its late 17th-century Baroque furnishings. The most striking is the altarpiece, carved in 1698 by Anders Ekeberg, who also made the pulpit. The font, of red limestone, dates from 1659 and is older still. Twelve chandeliers hang in the church interior, the oldest reputedly brought home from the Thirty Years' War in 1608 by a colonel named Thomas Muschkamp.
The church has had a succession of organs. An earlier instrument was sold on in the 18th century, and the organ case visible today, made by Jonas Wistenius of Linköping, dates from 1759, though it may instead derive from an 1867 instrument by local builders Sven and Erik Nordström — sources differ. The main organ itself was built by Nils Hammarberg of Gothenburg and installed in 1967, later enlarged in 1999.
In more recent times, the church has featured in national broadcasting, including a Christmas morning service broadcast by Swedish Radio in 2015.