Over a year ago, the global pandemic compelled higher education institutions in Pakistan to rapidly shift to digital learning, marking students’ first extensive exposure to e-learning. This study investigates how medical, dental, and allied health students in Pakistan perceive and respond to this transition. A nationwide descriptive, cross-sectional study was carried out. Participants were invited to complete a pre-validated, anonymous online questionnaire covering demographics, prior e-learning experience, perceived advantages and disadvantages, and overall attitudes toward e-learning. Descriptive statistics summarized all demographic data. The Chi-square test was applied to assess differences in perceptions between pre-clinical and clinical students, as well as to compare category-wise positive and negative responses. Additionally, associations between participant demographics and their perceptions of e-learning were evaluated using the Chi-square test. The study included 1,200 participants, of whom 797 (66.4%) were pre-clinical students and 403 (33.6%) were in clinical years. Across the cohort, the most frequently cited benefit of e-learning was a “comfortable learning environment” (70%), whereas the predominant drawback was “technical difficulties with IT equipment” (89%). Pre-clinical students primarily reported “anxiety stemming from social isolation” as a major challenge (p < 0.05), while clinical students highlighted “insufficient patient interaction” as their key concern (p < 0.05). Overall, 72% of respondents expressed a negative perception of e-learning. Following over a year of online education, medical and allied health students in Pakistan have reported significant dissatisfaction with e-learning. To improve engagement and alleviate stress related to the pandemic, initiatives such as faculty and student training, counseling programs, and the adoption of innovative teaching strategies should be implemented.