After ICTP work, Hoodbhoy returned to Pakistan to join Quaid-e-Azam University (QAU) where he began teaching and lecturing on physics. Eventually, he became chairman of Institute of Theoretical Physics (now department of physics). After spending more than 30 years at Qau, Hoodbhoy moved to Lahore where he joined the Lahore University of Management Sciences as a visiting professor, while remains a visiting scientist at the Stanford Linear Accelerator Center. Controversy over his contract in LUMS sparked an academic debate when it was reported in the news media that Hoodbhoy's email to Vice-Chancellor of LUMS was made public. Eventually, Hoodbhoy moved to Forman Christian College University permanently and joined the senior staff to instructed courses on physics.