The COVID-19 pandemic has affected people from almost every walk of life in general and academia in particular. It had a huge impact on teaching and learning resulting in a sudden shift from classroom and face-to-face teaching to distance and online teaching and learning. This sudden shift created a lot of ruckuses in the teaching of engineering disciplines. This study is pertinent to the examination of faculty perceptions of online teaching in Pakistani universities and the obstacles they face in teaching engineering students through the online mode during this pandemic. The research takes a quantitative and sample survey approach. A Google form questionnaire was used to collect the data from a sample of 91 faculty members from the engineering discipline of different universities in Pakistan during 2022. According to the study’s findings, faculty generally have a favorable opinion of virtual teaching in the context of COVID-19 for closing the achievement gap and guiding students’ futures in difficult times. However, they ran into a number of challenges when teaching online, including technological difficulties, problems with student participation, challenges with online tests and assessments, etc. The results of this study will urge educational institutions and policymakers to use the most up-to-date instructional methodologies and offer teachers ongoing professional development in order to improve the quality of online teaching, learning, and assessment in universities. Previous studies discussed a number of obstacles faced by students in virtual teaching in higher education, overlooking the perception and challenges faced by the engineering faculty. The present study replenishes this gap.