The COVID-19 outbreak led to a remarkable shift in teaching methods, forcing educational institutions to swiftly move from physical classrooms to digital platforms. In this regard, E-examinations became a crucial mode of evaluation during pandemic. This research aims to explore challenges faced by educators in higher education institutions, and examine potential gender-based differences in perceived difficulties. From 51 Higher Education Institutions (HEI) in West Bengal, 116 teachers (49 female and 67 male) participated in the study. Using Google Forms, data were collected and analyzed with six distinct codes to categorize the challenges expressed by the teachers. During online examinations, six major challenges encountered were: managing answer scripts and administering exams, invigilation and evaluation, network connectivity, overall planning and implementation, and technological equity and access. Predominant tools used for online examinations: laptops, mobile devices, and computers or tablets. Primary challenges highlighted by teachers are mainly: administration of examinations and management of response scripts and the ethical implications of online examinations. This research offers insights highlighting the need for further in-depth research, possibly integrating qualitative or mixed-methods approaches. The implications of these findings may inspire practitioners, and policymakers to enhance online examination procedures with cutting-edge tools and techniques. Moreover, the study strongly advocates for crucial measures to address identified challenges, fostering a seamless and equitable online examination experience for educators and students.