The name Kilian is derived from the Irish Gaelic name Cillian, which originated from the Latin word "cella" meaning "cell" or "chapel". It is believed to have first emerged as a personal name in the early medieval period, around the 5th or 6th century CE, when Christianity was spreading across Ireland and monastic communities were being established.

One of the earliest recorded bearers of the name was Saint Kilian, an Irish missionary who lived in the 7th century. He is known for his efforts in spreading Christianity throughout the Franconian regions of present-day Germany, where he was ultimately martyred around 689 CE. The town of Würzburg, where he was killed, became an important center for the veneration of Saint Kilian.

Throughout the Middle Ages, the name Kilian gained popularity among Irish and Scottish communities, particularly those with ties to monastic traditions. It was also adopted in various forms across parts of continental Europe, such as the German "Killian" and the French "Killien".

Notable historical figures with the name Kilian include Kilian of Passau, a 7th-century Irish missionary and bishop who helped establish the Diocese of Passau in present-day Germany. Kilian Stumpf (1655-1720) was a German Jesuit missionary and explorer who traveled extensively in Central and South America, mapping regions and contributing to geographical knowledge.

In the 19th century, Kilian Rudinger (1801-1871) was a German Catholic priest and writer who published works on topics ranging from literature to theology. Kilian Kirchhoff (1892-1981) was a German sculptor known for his monumental works, including the famous "Kreuzwegrelief" at the Benedictine Abbey in Maria Laach, Germany.

In more recent history, Kilian Jörg (1940-2008) was a German writer and playwright whose works often explored themes of identity and social critique. His plays were widely performed across Europe and received numerous awards and accolades.