Background There are serious concerns regarding the effectiveness of medical education in its current format during serious crises like the COVID-19 pandemic. Objective To explore academic, financial, psychological, & hygienic impact on medical students. Methods A cross-sectional, questionnaire-based study of students at different medical schools in Jordan. It included both basic and clinical years. Results There were 415 responses. Females constituted 51.8%. Around 50% of the participants were from the 6th year (n = 194, 46.7%). University of Jordan students represented around 40% of the responders. 60% of the students have GPA (Grade Point Average) of less than 3 points. Nearly half of the students indicated that their academic grades were affected during the pandemic. Clinical years’ students (51.0%) were more likely to be negatively affected than students in basic years (36.1%), P value 0.026. Sixty three percent reported that they sanitize their hands before touching eyes, nose, or mouth. More than two thirds (70.4%) of students indicated that their mental health was affected in the pandemic. Financial influence was a major aspect in around 53% of students and 34% of students were not able to pay the university fees due to the pandemic. The pandemic affected the elective training course location of 70.9% of respondents. Mental health was affected in 70.9% of students and 65.1% became more anxious or depressed with no significant difference among gender and academic years (P values 0.256 and 0.516, respectively). Students in the clinical years were more afraid of getting the infection than students in the basic years, however this difference was not statistically significant (p = 0.084). Conclusions Covid-19 Pandemic negatively affected the academic course of the medical students especially at the clinical training years’ level across Jordanian universities. COVID-19 pandemic left a negative impact on psychological & mental health of the students, too, rendering them more anxious, depressed, and afraid of coming to the hospital and handling patients.

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