Background: Medical and pathology education has gone through an immense transformation from traditional face-to-face teaching mode to virtual mode during the COVID-19 pandemic. This study evaluated the effectiveness of online histopathology teaching in medical education during the 2020 COVID-19 pandemic in Griffith University, Australia. Methods: Second-year medical students (n = 150) who had previously completed one year of face-to-face histopathology teaching, completed an online questionnaire rating their learning experiences before and during the COVID-19 pandemic after the completion of their histology and pathology practical sessions. The students' histopathology assessment results were then compared to the histopathology results of a prior second-year cohort to determine if the switch to online histopathology teaching had an impact on students' learning outcome. Results: A thematic analysis of the qualitative comments strongly indicated that online histopathology teaching was instrumental, more comfortable to engage in and better structured compared to face-to-face teaching. Compared to the previous year's practical assessment, individual performance was not significantly different (p = 0.30) and compared to the prior cohort completing the same curriculum the mean overall mark was significantly improved from 65.36% ± 13.12% to 75.83% ± 14.84% (p < 0.05) during the COVID-19 impacted online teaching period. Conclusions: The transformation of teaching methods during the 2020 COVID-19 pandemic improved student engagement without any adverse effects on student learning outcomes in histology and pathology education.