The stone citadel of Vologda began construction on April 28, 1566, by the order of Ivan IV the Terrible on the day of the holy apostles Jason and Sosipater. This event gave the fortress a second name, Nason-city. An English engineer, Humphrey Lock, was invited to lead the construction, although other sources claim it was the Russian engineer Razmysl Petrov. The tsar planned to create his residence here. The Kremlin was bordered by the Vologda River to the north, with moats dug to the southeast and south, while the western boundary ran along the modern Leninsky Street, where there were also moats and earthen ramparts. Water for the moats was supplied from the Sodyma River, whose course was likely altered. Construction ceased in 1571 after the unexpected departure of the tsar from Vologda. By that time, a stone wall with nine towers had been erected on the southeastern side and two towers with spans on the southwestern corner. Inside the citadel, the stone Sophia Cathedral and a wooden royal palace with the church of Joachim and Anna were built. After the tsar's departure, a wooden stockade with 21 or 23 tent-like towers was erected on the site of the unfinished walls. The wall was completely stone on the southeast and partially on the northwest. Despite its incompleteness, the Kremlin impressed with its size.

In the 1657 description, it was mentioned that the wooden walls on the northern and western sides were already gone, and the stone towers and walls were severely damaged. The fortress lost its significance, and stone and brick were used for the construction of churches and civil buildings. After the flood of the Vologda River in 1670, which eroded the earthen rampart from the Water Gate to the Ilyinsky moat, the fortress was no longer restored. In 1780, part of the stone towers still existed, but in 1822 and 1823, under Governor-General Brusilov, the last tower, the Gunpowder Tower, was dismantled during the creation of boulevards. The moats on the modern October and Leninsky streets were filled in.

The first general plan of Vologda from 1780 was based on the preserved stone walls of the Kremlin, the territory of which became the compositional center. From it, radial streets radiated: Central Street, Pyatnitskaya began from the Sophia Cathedral, the Eastern radial street went from Cathedral Square along Bolshaya Blagoveshchenskaya Street, modern Batyushkov Street, and Glinkovskaya Embankment, Mira Street. Petersburg, Leninsky Street was to become the western radial street.

In the 20th and 21st centuries, the territory of the Kremlin serves as a historical and commercial center of Vologda, known as the City or Nason-city. Traces of defensive structures can be seen in the form of moats, ponds of the VRZ park, the Zolotukha River, the rampart in the VRZ park, and in the foundations of the trading rows on Mira Street.

In 2011, Vologda archaeologists conducted excavations at the site where the Prechisten and Stone towers were located, as well as the spans between them. Soon, the discovered fortress will be included in the federal register of monuments. It is planned that the artifacts found during the excavations will be exhibited starting in 2013 at the Vologda Historical and Architectural Museum-Reserve.