In 1503, Grand Duke Ivan Vasilyevich took control of a third of the Ryazan cities, including Tula. From this moment, Tula became forever part of the Moscow principality. To protect the route to Moscow from the threat of the Crimean Horde, Vasily Ivanovich ordered the construction of an oak fortress in Tula on the left bank of the Upa River in 1507, leaving the old settlement by the Tulitsa River. The wooden fortress was shaped like an elongated semicircle and was equipped with German and Moscow firearms and cannons. Its construction was completed in 1509, and it stood for 231 years. In 1514, inside the oak fortress, following the example of the Moscow Kremlin, Vasily ordered the construction of a 'stone city,' which was completed by 1520-1521. The Resurrection Chronicle mentions the construction of the Kremlin in 1509: 'By the command of Grand Duke Vasily Ivanovich, a wooden city was built in Tula, and in the fifth year, a stone city was established.' In 1552, the city was besieged by the army of Crimean Khan Devlet I Girey while Tsar Ivan the Terrible was on a campaign against Kazan. The garrison of the Kremlin and the city militia held the defense until reinforcements arrived from Kolomna. In memory of these events, a cornerstone was laid at the Ivanov Gates of the Tula Kremlin. In the second half of the 16th century, a posad fortress appeared around the stone Kremlin, a wooden fortress whose area was ten times larger than that of the stone Kremlin. This territory was then the border of Tula. In 1605, a bell notified the residents of the arrival of False Dmitry I, and Tula became the pseudo-capital of the Russian state for two weeks. Nobles, gentry, Cossacks, and other serving people came to the Kremlin to swear allegiance to the impostor. In 1607, during the peasant war, the leader of the rebels, Ivan Bolotnikov, found refuge in Tula. That same year, the troops of Tsar Vasily Shuisky besieged the leaders of the peasant movement, Ivan Bolotnikov and Ileyka Muromets, who was posing as 'Tsarevich Peter.' The Kremlin endured a long siege but was taken due to the cunning of a boyar's son, who suggested that the Tsar's army fill the Upa River with bags of earth to create a dam. The water flooded the Kremlin, and the rebels capitulated. In memory of these events, an obelisk was erected in the Tula Kremlin in 1953. All this time, the Kremlin served as a home for the people of Tula. According to the scribal books, by the end of the 17th century, there were 107 courtyards and 197 residents in the Tula Kremlin. The first street of Tula was also located in the Kremlin and was called Bolshaya Kremlovskaya.

After the reunification of the left bank of Ukraine with Russia in the mid-17th century, the Kremlin lost its significance and ceased to be listed as a fortress during Peter's time. Repair works in the Kremlin were carried out in the late 18th and 19th centuries; in the 1930s, all dilapidated buildings were removed from the Kremlin walls, in the 1950s, partial repairs were conducted, and in the mid-1960s, a comprehensive scientific restoration began to restore the original appearance of the Kremlin. In 2012, the charitable foundation 'Tula Kremlin' was established, which has 1,648 benefactors who donated funds for the restoration of the Kremlin. In the same year, drainage was conducted from the Odoevskaya Tower to the Water Gate Tower at the expense of the foundation. In 2013, restoration and improvement works were carried out on the trading rows, a new tent was installed on the Naugolnaya Tower, and the battlements on the wall between the Nikitskaya and Ivanovskaya Towers were restored. The Assumption Cathedral was also restored, its facade became gray, and the domes were covered with gold. From 2012 to 2014, a large-scale reconstruction of the walls was carried out, and the electric station that had been located there since the early 20th century was removed from the territory. During this period, the bell tower of the Assumption Cathedral, which was destroyed in the 1930s, was also reconstructed. In 2017, the former substation was converted into the 'Exhibition Center of the Tula Kremlin.' The complex includes four exhibition halls: the Museum of Military History of the Tula Region, the Museum of Folk Art of the Tula Region, the Museum of Samovars and Tula Gingerbread, and the Museum of the History of the Tula Kremlin. There is also a 'free' hall for temporary exhibitions, forums, meetings, and conferences. On November 10, 2016, the President of Russia signed a decree to celebrate the 500th anniversary of the Tula Kremlin in 2020. On September 8, 2018, the Kazan Embankment was opened, hidden from the residents and guests of the city for more than half a century. In April 2019, as part of the All-Russian Forum 'Kremlins of Russia and Their Role in the History of the Russian State,' a museum of archaeology stylized as archaeological excavations was opened in the Tula Kremlin. The museum contains artifacts found during the reconstruction of the Kremlin from 2012 to 2015.