No written evidence has survived to our time regarding the origin of the kremlin, but according to the official version, the city of Kazan was founded in the early 10th century. Initially, the kremlin was called Kerman. There are no written sources on this matter.

The earliest archaeological finds were discovered in the northern part of the kremlin, closer to the Kazanka River, where an ancient Bulgar fortified settlement was located, and later, the fortress of the Kazan Khanate. Researchers disagree on the dating of the wooden fortifications: some believe that the Bulgar settlement was fortified as early as the 10th century, while others argue it was only in the 12th century. There are also disagreements regarding the nature of the fortifications: some believe that stone walls began to be erected in the 12th century, while others think this occurred only in the 15th or 16th centuries after the reconstruction of the kremlin by Ivan the Terrible's Pskov architects.

From the mid-13th to the first half of the 15th century, the kremlin became the center of the Kazan principality within the Golden Horde. In 1236, Mongol hordes led by Batu invaded Volga Bulgaria and destroyed its capital. By 1240, Bulgaria, like the Russian principalities, came under the rule of the Golden Horde. Some Bulgars resettled to the Kazanka area and founded Iske-Kazan, a city 45 kilometers from Kazan. In 1370, the Bulgar prince Hasan laid the foundation for a fortress on the site of the modern Kazan kremlin, which served as the residence of the Bulgar princes until 1445.

After the siege of Kazan by Ivan the Terrible in 1552, the fortress was destroyed. To build a new white-stone kremlin, the tsar invited Pskov architects Postnik Yakovlev and Ivan Shiryay. The fortress was significantly expanded, six stone towers were built, but in the 16th century, only a third of the wooden walls were replaced with stone. The complete replacement of wooden defensive structures with stone occurred in the early 17th century.

Pskov masters also erected the first Orthodox churches of the Kazan kremlin: the Annunciation Cathedral, the Church of Saints Cyprian and Justina, the Church of Dmitry of Thessalonica, the Spasskaya Church, as well as two monasteries, the Trinity-Sergius and the Spaso-Preobrazhensky. After the fire of 1672, brick construction began, and some towers, including the Spasskaya, were rebuilt by Moscow architects.

After the 1917 revolution, in the 1920s-1930s, during the struggle against religion, the bell tower and the cathedral of the Spaso monastery, the bell tower of the Annunciation Cathedral, the Church of Saints Cyprian and Justina, and the Spasskaya chapel were destroyed, and the iconostases and relics of the kremlin churches were lost. During the Soviet period, archaeological studies of the kremlin continued, which had begun in the 19th century. In the 1960s, the Tatar Restoration Workshop was established. With the formation of the Republic of Tatarstan in 1992, the Kazan kremlin became the residence of the President of the Republic of Tatarstan. In 1993-1994, directions for the reconstruction and development of the Kazan Kremlin complex were developed. In 1994, by the decree of the president of Tatarstan, the State Historical-Architectural and Art Museum-Reserve 'Kazan Kremlin' was established, and systematic scientific study and restoration of the complex began. The defensive walls and three towers were restored, and conservation and museification of 15th-16th century objects commenced. The construction of a mausoleum for the reburial of the khans' remains began. During excavations, the burial site of the Trinity Monastery and the necropolis of the Spaso-Preobrazhensky Monastery were discovered. The collapse of the Syuyumbike tower was halted. The governor's palace and the Palace Church were fully restored, as well as four buildings of the Cannon Yard. In the Archbishops' Court complex, the Cathedral Annunciation Cathedral was restored. In 1995, work began on the reconstruction of the Kul Sharif Mosque and the restoration of the interiors of the Annunciation Cathedral.

On November 30, 2000, at a session of the UNESCO World Heritage Committee, the Kazan kremlin was included in the World Heritage List. It combines the achievements of Tatar and Russian urban planning art, in memory of which a monument to the architects was erected in the square near the Annunciation Cathedral. The kremlin has been equipped with evening lighting, and panoramic views are available from the Millennium and Palace squares, as well as from the Kremlin embankment.