The parish of Värna is documented from 1361, with a priest named Kättilbjörn recorded in 1387. Before the present church stood here, there was likely a simple wooden church, though its exact location and form remain unknown. Sources differ slightly on the date of the current stone church: one account places its construction in the 1500s, while another suggests it was built of granite around 1500, so a precise date cannot be given with confidence.
The building underwent a major transformation in 1764, when the sacristy was demolished and walls moved to widen the chancel. A new entrance was created and a timber porch added, along with extra windows; the porch was later removed in 1952. Earlier, in 1728, the ceiling and walls had been decorated with paintings by Anders Wikström of Söderköping. A bell tower was added in 1860.
The altarpiece reached its present form in 1779, incorporating wooden sculptures said to originate from a medieval altar cabinet, made in Germany in the 15th century and associated with Grebo. A wooden panel bearing a biblical text was donated to the church in the 18th century. The altar rail, made of wood, dates from 1952 and is a copy of an earlier version.
Other notable furnishings include a pulpit made in 1723 and remodelled in 1836, and a font with a copper basin from 1734 set on a wooden stand made in 1952 to designs by the architect Erik Fant. A large bell was cast in 1764 by the bell-founder Elias Fries Thoresson of Jönköping and recast in 1947.
The church has had several organs over the years, including instruments from 1821 and around 1850, the latter originally built for a school in Eksjö. The current organ was supplied in 1948 by Åkerman & Lund, housed in an organ case dating from 1898, with a smaller choir organ added in 1992.