Teachers’ quality questions contribute to enhancing students’ existing thinking and reasoning skills. The practice of teacher questioning in the EFL reading classroom is critical in supporting student learning, especially in such contexts where there is limited research on these issues as in Indonesia. This study investigated the practice of teacher questioning and teaching reading in secondary schools in Indonesia. Teachers from three grade 11 classes from three different secondary schools participated in this multiple-site case study which was employed to generate rich explanatory data across sites. Data were gathered from the teachers in the form of observations, interviews, and textbook analysis. The findings from this study show that the teachers relied on the textbooks for pedagogies for teaching reading and for the kinds of questions they asked to assist in reading comprehension. The teachers were exposed mainly to low-level questions. Thus, they faced some challenges in generating high-level questions in these conditions, and required assistance in order to do this. The study provides important information about the practice of questioning strategies in a foreign language context in Indonesia and put forward implications for changes in reading lessons.