Online learning can play a significant role in continuing the teaching-learning process, especially during the pandemic. Moodle platform is one of the online learning solutions which is free. It is essential to justify and study student reactions, problems, and challenges using a Moodle-based online learning system for further successful online learning. This study aimed to investigate the EFL student challenges, issues, and reactions to the Moodle-based online learning system. The data were collected from 40 graduate and undergraduate EFL students from a private university in Central Java, Indonesia, through a questionnaire-based online survey. The data were analyzed using descriptive statistical techniques. Results of the study have shown that the most common challenges faced by the students were slow internet connection, over-loaded assignments with limited submission time, and health issues. Students believed that a slow connection increased their stress level. Besides, this study has revealed that the teacher's support was crucial in online learning using the Moodle-based system.