Favorable natural environment of the Celje area was appreciated by its inhabitants as early as in the pre-Roman and especially in the Roman period. It is therefore hardly surprising that during the Hallstatt period, the first settlement called Keleia was founded at the lowest point of the eastern part of Lower Savinjska Valley. In the Roman period, during the reign of Emperor Claudius (41-45), the settlement then called Municipium Claudia Celeia was granted town rights and saw its first apex. During the great migration period (5th ad 6th century), the town was razed, but only to be rebuilt in the early medieval period. The medieval Celje (Cylie) was first mentioned in the Admont Chronicles written between 1122 and 1137.

In the late medieval period, a lasting impression was given to Celje by the successful and ambitious dynasty of the Lords of Sanneck (Žovnek), later to become the Counts of Celje. Although they only ruled for a short period of time, their political dexterity led them all the way to the top of European politics of the period. Their daughters wedded European kings and emperors and the Sannecks (Žovneks) who were first awarded the title of Counts and then of Grand Princes chose to reside in Celje. Initially, they dwelled in the Upper Celje (Old Castle); around the year 1400, they moved to the new renaissance building located in the town, called the Lower Castle. As a settlement, Celje gained a lot by their presence. On April 11th 1451, Frederick II, the Count of Celje, granted city rights to Celje, including all town privileges; in the decades to follow, Celje was fortified with city walls (completed in 1473), a must in that time, and a defense trench.
Following the death of the last Count of Celje, Ulrich II (1456), the property of the Counts of Celje fell into the hands of the Habsburg royal house. In this period, Celje was one of the major renaissance centers in the territory of present-day Slovenia; hence, a real city life with highly developed trade and craft developed in the town that became the center of the Celje Quarter. Protestantism, the danger of Turkish invasion, and natural disasters – three aspects of the life at the time that agitated the morally, economically, and politically devastated Europe, were also felt in the city on Savinja.

Despite the hardship, the city carried on with its life. At the end of the 18th century, Celje went through a new renaissance. Bearing the flag of the new area was the city walls yielding to urbanization and early modern industry at the end of the 18th century. When the first train arrived to Celje in 1846, the town still enjoyed relative peace and quiet of a Biedermeier atmosphere. Simultaneously with other parts of the Austrian Central Europe, Celje too was affected by the spring of nations in the second half of the 19th century, which aggravated the tension between particular nations within the Habsburg monarchy and ultimately led to its dissolution following the First World War.

The end of World War I in 1918 brought a new momentum to the town on the Savinja River. A new political framework, different political ideas and notions, and new spiritual encounters swayed the mentality of the citizens, changing their lives in many ways. World War II and occupation also left deep cuts on Celje and its people, some of which have remained unhealed to this day. Nevertheless, like so many times before, Celje rose from the ashes and bloomed again.
Following WWII, the city on Savinja developed into a lively industrial and trade center; in addition, it has remained to this day the center of the municipality with all characteristics of a regional administrative, business, cultural, educational, healthcare, and tourist center. In recent years, Celje has been deemed as the fastest developing city in Slovenia.