This study aims to investigate the influence of teacher’s questions on students’ reading comprehension and the latter’s perceptions of the impact of these questions on their reading performance. This mixed method study was conducted with 14 grade 9 teachers and 569 students under these teachers to examine the influence of questions on reading comprehension. On the other hand, 14 students, one representative from the class of each teacher, were selected to participate in the retrospective discussion to explore their perceptions of the influence of the questions on their reading comprehension performance. The instruments used were an observation checklist, multiple-choice question (MCQ) test, and a discussion guide to capture the teacher’s questions, reading comprehension performance, and perceptions of students, respectively. The results for the quantitative part indicated that an increase in the number of teacher’s questions was positively correlated with an improvement in students’ reading comprehension performance. However, it was observed that teachers predominantly focused on lower-order thinking (LOT) questions resulting in students’ better performance on tests that assessed LOT skills but struggling on tests that required higher-order thinking (HOT) skills. Considering the perceptions of students on the teacher’s questions and their influence on their comprehension, they recognized the importance of relevant questions in maintaining engagement. They also expressed a preference for open-ended questions that encourage discussion and promote critical thinking. The connection between the findings from both quantitative and qualitative aspects suggests that by incorporating more (HOT) questions into their teaching practices, teachers can enhance students’ reading comprehension abilities.