The COVID-19 pandemic has had major impacts on various fields of life, including education. This situation causes a change in learning from face-to-face learning to e-learning which is carried out at home. E-learning carried out at home makes students difficult during the learning process and this can be seen from low outcomes of science learning. This study aimed to identify students' learning difficulties in e-learning-based science. The research was carried out in the even semester of the 2020/2021 academic year. The population in this study were seventh-grade students of SMP Randudongkal Pemalang Regency as many as 700 students. The sample was calculated using the Slovin formula of proportional random sampling and obtained 254 students as sample. The instrument used in the study was a questionnaire using a google form application, interview sheets, and documentation. The data analysis was carried out using descriptive quantitative and qualitative analysis. The results of the study indicated that the internal factors causing student learning difficulties were still relatively high. The percentage of these internal factors showed health (65.03%), learning motivation (66.14%), learning concentration (61.81%), affective (68.28%), learning habits (68.09%). External factors that cause student learning difficulties were also still relatively high. The external factors that cause learning difficulties were the teacher explanation(69.11%), home-practice(61.17%), internet quota (63.29%), internet access (66.81%), devices (68.21 %), use of applications (75.05%), books/references (60.93%), and parents (77.59%).