In recent times, online teaching and assessment have provided a great opportunity to explore better methods in medical education. There are inconsistent views concerning the effectiveness of online assessment. Hence, the present study aimed to evaluate online teaching and assessment methods in relation to face-to-face methods by comparing students’ performances. The students’ assessment results in two basic anatomy courses, which are part of the Doctor of Medicine and Biomedical Sciences programs at Sultan Qaboos University, were analysed. We compared the students’ mean scores and coefficient of variance in the multiple-choice written exams and the objective structured practical exams during the spring semesters of 2019, 2020, and 2021, containing face-to-face teaching and exams, partial online teaching and online exams, and online teaching and both proctored online and face-to-face exams, respectively. The sudden transition to online teaching and assessment halfway through the semester resulted in higher means and a lower coefficient of variance among students’ scores in both theory and practical exams. However, when the fully adopted online method of teaching and assessment was employed, the mean scores decreased, and the coefficient of variance increased to figures close to those witnessed before the pandemic, when teaching and assessment were face-to-face. This trend applied to both the Doctor of Medicine and Biomedical Sciences programs’ anatomy courses. The results indicate that online assessment of theoretical and practical anatomical knowledge is comparable to that of face-to-face assessment. However, proper planning and preparedness are mandatory to achieve the desired outcomes.