Background Croatia has closed all educational institutions after 32 cases of SARS-CoV-2 infection were confirmed and switched to exclusive e-learning. Health sciences university students may have been particularly affected with this change due to a lack of practical education. It is not known how health sciences students and schools have adjusted to exclusive e-learning. This study aimed to explore attitudes and concerns of health sciences students in Croatia regarding the complete switch to e-learning during the COVID-19 pandemic. Methods Eligible participants were students from 9 institutions offering university-level health sciences education in Croatia enrolled in the academic year 2019/2010, and participating in e- learning. Data were collected with a questionnaire distributed via email during April/May 2020. Results A total of 2520 students (aged 25.7 ± 7.7 years) responded to the questionnaire (70.3% response rate). General satisfaction with exclusive e- learning was rated with average grade of 3.7 out of 5. Compared with previous education, exclusive e-learning was rated with average grade of 3.2 out of 5. Compared to classroom learning, equal or higher motivation to attend exclusive e- learning was reported by 64.4% of participants. With a longer duration of exclusive e-learning, equal or higher motivation was reported by 65.5% of participants. Less than half of the students indicated they felt deprived or concerned due to the lack of practical lessons. Most participants indicated that in the future, they would prefer to combine classic classroom and e-learning (N = 1403 ; 55.7%). Conclusions Most health sciences students were satisfied with the exclusive e-learning, as well as their personal and institutional adjustment to it. Students’ feedback can help institutions to improve the exclusive e-learning experience for students in the time of the pandemic.