English as a Foreign Language education has long emphasized learner autonomy. Formally, the teacher should encourage students to develop autonomy in both English and general life. However, Indonesian EFL teachers had to deal with some challenges in promoting learner autonomy. This study, therefore, aimed to investigate EFL teachers' challenges and explore teachers' strategies to promote learner autonomy in the pandemic era. This study employed a qualitative approach, more specifically a case study. Six EFL junior high school teachers in Kesugihan District, Cilacap, participated in this research. They were selected based on their consideration of teaching the grade nine and having more than five years of teaching experience. The researcher used primary data from interviews and secondary data from classroom observation and field notes to collect qualitative data for this study. The thematic analysis was used to analyze the data. The results of this study revealed that students' motivation in completing the task, reward-oriented, students ‘ability to learn independently, parents' economic status, teacher personality, teacher competence, zoning school systems, teaching time, minimum mastery criteria, unscheduled events, workload, colleague conflict, and the status of English as a foreign language contributed to the challenges faced by EFL teachers in promoting learner autonomy during the pandemic era. EFL teachers have used strategies to transform challenges such as providing affective support, improving the teacher's personality and creativity, and providing a classroom learning activity to promote learner autonomy. Further research is recommended to investigate the external factors, such as the minimum mastery criteria.