The objective of our study was to evaluate dental students’ perception of the challenges faced during the COVID-19 pandemic related to their clinical work, education, performance, online examinations, psychological health, and teamwork. A validated online questionnaire consisting of closed ended questions was sent to all the undergraduate dental students at our institute. Data were collected and analyzed statistically using a chi-square test to compare responses of male with female and junior with senior students. A total of 317 undergraduate dental students (N = 317) participated in this cross-sectional study. The most common challenges perceived by the participants were related to their exam duration (77.3%), patient availability (66.9%), difficulty in understanding online lectures (58.4%), and a fear of losing grades (57.4%). Participants reported that the COVID-19 pandemic affected their performance in the courses (75.4%), teamwork (72.2%), educational aspects (67.5%), and psychological health (51.1%). A significantly greater proportion of female students reported the adverse effects of COVID-19 on their psychological health than male students (p = 0.031). Senior students perceived the negative impact of COVID-19 on teamwork significantly more than the junior students (p = 0.004). The majority of students reported challenges during the COVID-19 pandemic. Female students and senior students perceived more challenges than their counterparts. Future studies from other institutes of this region are recommended to establish a clearer picture of COVID-19 related challenges faced by dental students.