The COVID-19 pandemic has affected all aspects of daily living, including the provision of quality education. Providing quality education led to the shift from face-to-face method to online delivery of instructions. It is the purpose of the study to find out the challenges encountered by students of Masters of Education in a Higher Education Institution in order to come up with solutions that may improve the online teaching of faculty. The researchers made use the descriptive survey design to identify the challenges experienced by the respondents. Data were analyzed using the correlational statistical tools: Pearson Product-Moment Correlation and the Independent Sample t-test. Results showed challenges encountered in online teaching are related to school and teacher factors. There were no significant differences in the challenges experienced by the respondents when grouped by age, gender and years of service/teaching. Recommendations were focused on the improvement of school facilities and faculty support on development, improvement of knowledge and skills and updating/upgrading of current academic structures and pedagogies to support online education.