The nature of the region offered good living conditions to its inhabitants even before the ancient Roman times. It is therefore hardly surprising that the settlement then called Keleia was established in the eastern part of the Savinjska Valley, at its lowest elevation point, as early in the Hallstatt period, and during the era of the Celts. In the Roman period, during the reign of Emperor Claudius (41–45), the settlement, called Municipium Claudia Celeia, was granted town privileges, leading the town to its first heyday. During the great migration of the 5th and 6th century, the town was razed, only to be reconstructed in the early mediaeval times. The first reference to Celje of the Middle Ages (Cylie) is found in the Admont Chronicles written between 1122 and 1137.
In the late Middle Ages, the short reign of the Žovnek (Sanneck) nobles, later elevated to the Counts of Celje and Princes, whose shrewd political actions allowed them to reach the very top of the European politics of the time, left a permanent imprint on the town. Their daughters married European kings and emperors. The Lords of Žovnek (Sanneck), first elevated to the ranks of immediate counts and then to princes, chose Celje as their seat. Initially, they resided in the Old Castle; but around 1400, they moved to the new renaissance building in town, called The Lower Castle. The settlement of Celje gained a lot in the period. On April 11, 1451, Friderik II, the Count of Celje, bestowed town privileges to Celje, including all relevant rights. In the decades to follow, the town walls (completed in 1473) and the defensive ditch were built.
After the death of the last Count of Celje, Ulrik II (1456), the dynasty's property was inherited by the Habsburgs. At the time, Celje was one of the most notable renaissance centres on the territory of present-day Slovenia. True urban life with highly developed trade and crafts started to flourish in the town that became the centre of the "Celje District". The town on the Savinja river was also shaped by contemporary spiritual movements (Protestantism), Turkish invasions, and natural disasters, all of which troubled the morally, economically, and politically devastated Europe in those times.
Against all odds, the city persisted, seeing a new renaissance at the end of the 18th century. Presaging the new era, the town walls had to yield to urbanization and early modern industry late in the 18th century. When the first train arrived in Celje in late 1846, the town was still enjoying its tranquil Biedermeier atmosphere. In the 2nd half of the 19th century, Celje, like other parts of the Austrian-ruled Central Europe, saw the national awakening that led to escalation of national conflicts towards the end of the century, and eventually to the demise of the centuries-old Habsburg monarchy after World War I.
After World War I, the city on the Savinja River saw new changes. A new political framework, a different set of political views and agendas, and new spiritual movements affected the mentality of the people and changed the lives of Celje residents in many ways. World War II and occupation, too, inflicted deep wounds on Celje, which have not healed to this day. But yet again, Celje rose from the ashes and flourished again.
After World War II, it developed into a lively industrial and commercial centre. Moreover, as the seat of the Municipality, it has all the characteristics of a regional, administrative, business, cultural, educational, healthcare, and tourist centre. In recent years, Celje has been the most rapidly developing city in Slovenia.