Aim: In the current situation of COVID-19 pandemic, personal protective equipment has to be mandatorily worn by dental professionals all times in the dental clinical settings. The aim of this study was to assess the physical discomforts and related health issues faced by dental professionals while wearing personal protective equipment in dental clinical settings during the pandemic. Methods: This was an online cross-sectional survey conducted in November to December 2020 among dental professionals of various regions of country. A prevalidated questionnaire was sent through email/WhatsApp groups to 650 dental professionals. Informed consent was taken from all the participants. Information was collected about the demographics, type of dental set-up, average daily working hours, types of PPE worn, physical discomforts related to the various procedures in dentistry. Association was analyzed between demographics and the discomforts using Chi-square test. Results: A total of 309 dental professionals (163 females, 146 males) from all parts of the country responded to the online questionnaire. Maximum respondents were postgraduates or pursuing MDS (79%), majority (42.1%) were pediatric dentists followed by general dentists. Sweating, difficulty in vision, difficulty in breathing, and headache were the common discomforts reported by majority of the respondents. Headache and difficult breathing were more significantly associated with female dental professionals (p < 0.05). N95 wear was associated with breathing difficulty (56%) while use of faceshield led to the discomforts in visual acuity in 46% respondents. Conclusion: The survey has depicted several challenges and various physical discomforts being experienced by the dental professionals during this pandemic. Although wearing PPE is associated with difficulties to dentists but it is extremely essential to wear PPEs for self-protection during the ongoing pandemic.