Coronavirus-19 (COVID-19) is an emerging pandemic that has caused significant disruptions to education, resulting in marked scholar closures across the world. The present study documents the student perception of the online educational process at six universities in Saudi Arabia during the COVID-19 lockdown period. The individual variable factors, i.e., institution, sex, and blended learning, that might influence student perception were also investigated. In this respect, a questionnaire that assessed the impact of COVID-19 on the online learning process and student perception was emailed to a total of 17,230 students from 3 institutions (medical, applied health and dental students) affiliated with six universities in Saudi Arabia. Principal component analysis (PCA) was performed to determine the validity of the questionnaire. A total of 4850 (28%) students responded to the questionnaire and 46.9% (n = 2275) of the respondents were highly satisfied with their online education. Analyses of the scores from the students showed a highly significant difference (p = 0.000) between the male and female students. Applied health students (highly satisfied score = 63.13) were the most satisfied with their online education, while medical students (highly satisfied score = 39.3) were the least satisfied with this education. In addition, applied health, dental and medical students showed a significantly higher score in favor of blended learning after schools re-open (p = 0.000). Collectively, student satisfaction with online education was common, and blended learning was preferred over the traditional format by both genders and all the students. The present data provide interesting contributions and evidence for policy makers and implementers, which might be helpful for the judgment side of decision making.