The Covid19 Pandemic has shifted the entire momentum of the traditional education processes into an environment where students experience difficulties in the E-Learning program. This study determines the challenges encountered in the duration of the E-learning and its’ effect on students’ perceived learning and satisfaction during the Pandemic. The investigation study formulated an aggregate of 313 respondents on a snowball inspecting strategy. Frequency and simple percentage, weighted mean, Chi-Square Test of Independence, and Oneway ANOVA were used to treat and interpret the data. The findings revealed that the students encountered difficulties through course quality, peer interactions, learning diversification, user-friendliness, and course design. Additionally, it was revealed that how they perceived these difficulties affects their perceived learning and satisfaction in the E-learning process. It was found out also that a higher level of challenges would associate with dissatisfaction and lower student perception in education. The study concluded that E-learning is a platform that should be present in the teaching and learning modalities in all institutions regardless of the situation. Additionally, the course quality, peer interactions, learning diversification, user-friendliness of the process, and its course contribute to increasing the student’s perceived satisfaction in E-learning. Generally, the impact of the Covid 19 pandemic provides a manifestation that to improve student perceived learning and satisfaction; there is a need to intensify the execution in the administration, teachers, and the learning management systems used in a Higher Education Institution.