The development of Rijeka impelled the newly arrived Slavic settlers – the Croats – to conquer Tarsatica and start building a new settlement. The first original mention of the medieval settlement dates back to the first half of the 13th century when two settlements appear in historical sources: TRSAT, on the hill on the left bank of the Rječina River, on the site of the Liburnian settlement TARSATA and RIJEKA, on the shore, on the site of the Roman TARSATIKA. Rijeka was a small, fortified town, crammed inside its walls protected by several defensive towers, divided into two parts: the upper part with a medieval castle and St. Vitus church (which is where the name Flumen Sancti Viti came from), and the lower residential, commercial and crafts settlement called Rika or Rijeka by its inhabitants.

Both at the beginning and at the end of the 14th century, Rijeka was ruled by the Devin noblemen, the princes of Krk (later Frankopans), then by the Walsee family and, since 1466, by the Habsburg family. During that period Rijeka had around 3000 inhabitants. The considerable economic development began in the 16th century, owing to the  iron, oil, wood, wool, cattle and leather trade. In the 16th century, the town even had a printing house which printed books in the Croatian - Glagolitic script. At the time, the settlement on the left bank of the Rječina River, under Trsat, did not exist (Sušak). It was not formed until the 18th century.

The golden period of Rijeka’s commerce suddenly lost momentum in the second half of the 15th century. Frequent Ottoman attacks interrupted the traffic routes, as did the wars of the claimants for the Hungarian throne and the eternal conflicts between the Uskoci and the Venetians. The war began to pacify in the second half of the 17th century.

The arrival of the Jesuits in Rijeka and the foundation of their high school significantly improved education and cultural life, strengthening the Romanic influence to the detriment of the Croatian language and the Glagolitic script. Rijeka's economy began gaining significant advantage in the 18th century. That is when Emperor Charles VI proclaimed Rijeka a free port, but the soon-to-be strengthened Hungary, as a part of the Habsburg Monarchy, began to see Rijeka as its exit into the world. At the turn of the 18th into the 19th century, Rijeka was first under French and then once again under Austrian administration.