Rajić was born on September 21, 1726 in Sremski Karlovci. Jovan rceived his elementary education in his native town, in the school of Deacon Petar Rajkov, a more zealous than learned successor of his own imported Russian teachers, notably Emanuel Kozačinski. It was through Rajkov that young Jovan Rajić would learn Serbian historiography, which belonged to the latter group. He attended Novi Sad's Petrovaradinska roždestveno-bogorodičina škola latinosko-slovenska, the Latino-Slavonic Spiritual Academy for young theologians, founded by Russian-born Emanuel Kozačinski in 1731. In 1744 he moved to Komárom where he attended a Jesuit gymnasium for four years. Fearing to be converted, he became a student of Protestant lycée in Sopron in 1748. He graduated in 1752 and he was ostensibly headed for the church. But his tastes lead him in a different direction for the time being; not content with a knowledge of books only, he wished to know the world and people better. During a period of almost ten years he seized every opportunity for profitable travel whenever he could. He travelled on foot from Hungary to Russian Empire – a distance of 800 miles -— where he enrolled as a student of the prestigious Kyiv-Mohyla Academy. He remained in Kiev until 1756 studying theology. He immediately formed a friendship with his professors, many of whom were disciples of Feofan Prokopovich, the great reformer of the Russian Orthodox Church and one of the founders of the Russian Academy of Sciences. After graduating from the Kiev academy he travelled to Moscow and Smolensk. For the next few months he led an unsettled life, attracting attention everywhere by his talents and boldness of his teaching. On his way home he also visited Poland and various parts of Hungary. In 1757 he returned to his native Sremski Karlovci and sought a teaching position at a seminary called Pokrovo-Bogorodičina škola, which was denied. Dejected and hurt, he decided to go back to Imperial Russia. He arrived in 1757 back in Kiev where he stayed only for a short time. That same year he travelled to Poland, Wallachia, Moldavia before taking a ship across the Black Sea to Constantinople, and from there to Mount Athos, where he spent a few months at the Serbian Monastery of Hilendar, doing research in the library. It wasn't until late 1759 that he became a professor of geography and rhetoric in Pokrovo-Bogorodičina škola in Sremski Karlovci. Entering a conflict with high representatives of Serbian Orthodox Church in Sremski Karlovci, he moved to Temesvar, modern day Romania. Life at the episcopal residence was luxurious. Though Rajić resisted the evils attendant on such luxury—loose morals, drunkenness, intrigue—he did acquire a vice which was to embiter the rest of his days, avarice. But more important, he found time in Temesvar to work on his History. After a turbulent year and a half, Rajić left for Novi Sad at the invitation of the Serbian Bishop of Bačka, Mojsije Putnik. He was inaugurated rector of the institution of higher learning, Duhovna kolegija, by Metropolitan Pavle Nenadović of the Metropolitanate of Karlovci in 1767. There he stayed for more than four years as both rector and professor of theology. His lectures, in which he endeavoured to show that Orthodox theology is in complete harmony with reason, were received with eager interest by the younger generation of thinkers. His unshakable faith in Reason awakened and inspired his students and thus prepared succeeding generations to traverse paths which were closed to Orfelin and to his Serbian contemporaries. In 1772 he went to Kovilj monastery where, at the age of 46, Rajić became a monk and soon after he was elevated to the monastic rank of archimandrite, and made abbot of the same monastery. He spent the rest of his life in the monastery writing books, mostly with religious and theological themes. In a fruitful lifetime which spanned the last three quarters of the eighteenth century, Rajić brought Rationalism to its zenith among Serbs in Serbian lands.

He died in the Serbian Kovilj monastery on December 22, 1801.