Educational institutions, which are crucial to a nation’s development, are also adopting e-governance principles and best practices. It is vital to find out the opinions of main personnel of higher educational institutions regarding the challenges they face in implementing e-governance for efficient university operations. Data was collected from 32 participants (teachers, registrars, librarians) from eight universities in Pakistan. Researchers used semi-structured interview protocols to collect data. We carried out thematic analysis for conclusions through interviews. It is explored that e-governance is being implemented in various universities’ operations. Students are provided facilities of e-governance in admissions, academic matters, examinations, and library. Teachers are provided facilities of e-governance in salary disbursements, attendance, communication, online classes, examinations and grading. Moreover, to implement e-governance the departments of universities face internet-based infrastructural, financial, technological, human, and developmental challenges. Findings of this study may well be used by universities’ stakeholders and administrators to understand well about the current status of e-governance in the universities. Moreover, they may well be able to better understand what advanced digital tools can be used to enhance the efficiency of e-governance systems. This study highlighted the status and challenges of e-governance in Higher Education on the stakeholders of Pakistani universities.