Objective: This study aimed to identify the factors that affected health profession students' emergency transition during the COVID-19 pandemic and to explore strategies that may help students be better prepared for any future health crises. Participants: This study population included 73 students that were originally enrolled in one online section (n = 49) and one face-to-face section (n = 24) of a healthcare administration course before the transition. Methods: The cross-sectional study was conducted and the anonymous survey data were analyzed using SPSS and a Man-Whitney U test. Results: Of the 73 students, 48 completed the survey, with a response rate of 66% (48/73). There was a statistically significant difference in the perceived COVID-19 impact (z = -3.339, p = 0.001) and difficulty transitioning during the pandemic (3-2.142, p = 0.032) between both groups. The top three hindering factors were stress and anxiety, difficulty focusing on studying at home, and time management due to uncertainty. Conclusions: The study findings suggest strategies that may help students with adequate knowledge and capabilities in managing stress, anxiety, and unprecedented challenges in the future.