St. Kilian was first mentioned in documents in 1187 as a chapel in Erla, which belonged to the Veßra monastery. It was located near the village of Raasen, on the Breitenbach stream, and developed into a church mound with a choir tower church, rectory, hospital and other outbuildings as well as a cemetery. Until 1815, the village belonged to the Henneberg or Electoral Saxon district of Schleusingen and then passed to the Schleusingen district of the newly formed Prussian province of Saxony, where it remained until 1945. In 1929, the St. Kilian estate district was incorporated into the village. The rural community of Raasen was given the new name St. Kilian.

On October 3, 1991, St. Kilian was incorporated into the municipality of St. Kilian. This was incorporated into Schleusingen on July 6, 2018.

St. Kilian currently has around 210 inhabitants and is an attractive residential location as well as a commercial location for small businesses.