The monastery was founded in the 10th–11th century. After the fall of Bulgaria under Ottoman rule, it fell into decline. It was restored in the 17th century by St. Pimen of Sofia, but was burned down again at the end of the 18th century.
The relics of the Russian officer Nikolai Alekseyevich Kiryayev, born in Saint Petersburg, rest beside the wall of the old church. He was killed on July 6, 1876, between the villages of Rakovitsa and Vlahovich (today Podgore), fighting against the Ottomans for freedom.
In 1848, the first secular pedagogical school in Northwestern Bulgaria was opened at the monastery. It was established by Petraki Shishmanov from the city of Vratsa and the then abbot, Father Danail. They gathered 32 sons of merchants from across the Vidin Sanjak, who later became teachers after completing their education.
The monastery became an important center of national liberation movements. The Vidin Uprising of 1850, one of the largest during Ottoman rule, was organized here, as well as the Dimitraki Uprising of 1856.
The monastery has been declared a cultural monument and is today restored and fully active.
In 2002, with the blessing of the Metropolitan of Vidin, Dometian, the monk Antim settled in the monastery. Later, the novice Neofit joined him and was tonsured as a monk in 2004. Their spiritual father was Bishop Sionius of Velika. Antim was later elevated to the rank of archimandrite and appointed protosyncellus of the Vidin Diocese, as well as ephimerios of the Klisura Monastery.
The Rakovitsa Monastery later became a convent, headed by Abbess Kassiana, along with three nuns and one novice. In the spring of 2025, it became a male monastery again, after Monk Yakov from the “Joachim and Anna” Monastery in Bistritsa (Sofia) settled there. He followed his spiritual elder, the newly appointed Metropolitan of Vidin, Pahomiy. The entire sisterhood of the Rakovitsa Monastery moved to the Divotino Monastery near Bankya, under the jurisdiction of the new Metropolitan of Sofia and Bulgarian Patriarch Daniil (former Metropolitan of Vidin).
The monastery complex consists of two churches, residential quarters, and auxiliary buildings. The old church, built in the 10th century (8.5 × 8 meters), is of the inscribed cross type with a dome resting on a hexagonal drum, and a narthex added in the early 19th century. It was painted in 1825, and its valuable frescoes were restored in 1979.
After the Liberation, a new church with a tall bell tower attached to its western side was built in memory of those who died in the uprisings.