Among the yellowed texts are Newton's famous prediction of the apocalypse in 2060.
Newton revolutionized physics, mathematics and astronomy in the 17th and 18th century, laying the foundations for most of classical mechanics - with the principal of universal gravitation and the three laws of motion bearing his name.
However, the curator of Israel's national library's humanities collection said Newton was also a devout Christian who dealt far more in theology than he did in physics and believed that scripture provided a "code" to the natural world.
"Today, we tend to make a distinction between science and faith, but to Newton it was all part of the same world," said Milka Levy-Rubin. "He believed that careful study of holy texts was a type of science, that if analyzed correctly could predict what was to come."
So he learned how to read Hebrew, scrolled through the Bible and delved into the study of Jewish philosophy, the mysticism of Kabbalah and the Talmud - a compendium of Jewish oral law and stories about 1,500 years old.
For instance, Newton based his calculation on the end of days on information gleaned from the Book of Daniel, which projected the apocalypse 1,260 years later. Newton figured that this count began from the crowning of Charlemagne as Roman emperor in the year 800.
The papers cover topics such as interpretations of the Bible, theology, the history of ancient cultures, the Tabernacle and the Jewish Temple.
The collection also contains maps that Newton sketched to assist him in his calculations and his attempts to reveal the secret knowledge he believed was encrypted within.
The texts may be accessed here.