This study examined teachers’ perception on the challenges of using E-learning in teaching primary school pupils in this era of COVID-19 pandemic in Anambra State. Two research questions and one hypothesis guided the study. The study used survey design. The population for the study comprises of all the schools and teachers in Anambra State. Purposive sampling techniques was used to sample two Local Education Authorities, one for urban area and the other for rural area. Using stratified random sampling techniques, 5 schools were selected from each local education authority, making it 10 schools, with 30 teachers randomly selected (15 teachers each) from the two Local Education Authorities. A 36-item questionnaire developed by the researchers titled “Challenges of using E-Learning in Primary Schools (CEPS) was used to collect data. The questionnaire was validated by three experts. The reliability of the instrument was determined using Cronbach Alpha Formula. A reliability of 0.76 was obtained for the entire instrument. Data collected was analyzed using Mean (X) and Standard Deviation (SD). T-test was used to test the hypothesis at 0.05 level of significance. Findings revealed that inadequate fund among others are the challenges of using E-Learning and the provision of E-learning facilities among others are the possible solutions to the challenges of using E-learning in teaching primary school pupils in this era of COVID-19 pandemic in Anambra State. The finding on hypothesis shows that the null hypothesis was rejected. The researchers recommended among others that government and other stakeholders in education should provide E-Learning facilities in primary schools.