He returned to Israel as a researcher; he was the founder and first chair of the computer science department at Tel Aviv University. He became a professor of computer science at the Weizmann Institute in 1981. From 1999 until his death, Pnueli also held a position at the Computer Science Department of New York University, New York, U.S.
Pnueli also founded two startup technology companies during his career.
In 2000, he was awarded the Israel Prize, for computer science