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Background Adherence to preventive control measures is influenced by perception, attitudes, and practices toward the disease prevention. Aim To assess the perceptions, attitude, and practices of university students in three health sector faculties (Medicine, Nursing, and Pharmacy) from six Egyptian universities towards COVID-19 pandemic prevention. Methods An electronic online survey was distributed to students of 3 faculties (Medicine, Pharmacy, and Nursing) in six Egyptian universities from March to July 2021. The questionnaire consists of the following parts: socio-demographic data of participants, student perception and attitude towards the COVID-19 pandemic and its consequences, as well as practices of preventive measures in the community. Results The study included 1990 participants. Most respondents perceived the seriousness of the COVID-19 pandemic (88.2%). The rates of practicing precautionary measures were mostly high (approximately 90% or above). Significantly high attitude scores toward the pandemic were detected in people with quite-to-extremely concerned, very good/excellent status, aware of infection risk, willing to report positive cases and avoiding contact with them, and seeking medical advice regarding infection. The attitude to protective measures followed a similar pattern along with average health status, female students, and avoidance of contact when experiencing flu symptoms. Significantly higher practice scores were observed in those with bad health status, rural areas, perceiving the risk of infection, willing to report positive cases, and avoiding contact with positive cases. Conclusion The effectiveness of precautionary measures should be stressed to promote positive student practices.