Born in Nahalal, Israel, Pneuli received a Bachelor's degree in Mathematics at the Technion in Haifa, and PhD in applied mathematics from the Weizmann Institute of Science. His thesis was on the topic of "Calculation of Tides in the Ocean". He switched to computer science during a stint as a post-doctoral fellow at Stanford University. He returned to Israel as a researcher and after a sequence of academic appointments became a professor at the Weizmann Institute.
Pnueli has also founded two startup technology companies.
He is married and has 3 children and 1 grandchild.