Despite the growing emphasis on inquiry-based learning as an effective pedagogical approach for fostering higher-order thinking skills, empirical evidence examining how teachers’ actual classroom practices influence students’ analytical and evaluative abilities remains limited. This study aims to investigate the relationship between teachers’ implementation of inquiry-based learning and the development of students’ higher-order thinking skills, specifically analysis and evaluation, through a quantitative descriptive comparative design. A validated questionnaire was administered to a purposive sample of 150 teachers from two schools in the eastern province in Saudi Arabia: one implementing inquiry-based learning and the other adopting traditional instructional approaches, during the first semester of the 2024/2025 academic year. The comparative approach enabled an examination of differences between the two educational contexts. The instrument consisted of five main dimensions, including indicators of inquiry-based practices, analytical skills, evaluative skills, challenges faced by teachers, and teachers’ attitudes toward the strategy. Data were analyzed using the Statistical Package for the Social Sciences (SPSS). The findings revealed a statistically significant positive correlation between the degree of teachers’ use of inquiry-based learning and students’ acquisition of analytical and evaluative thinking skills. Furthermore, comparative results indicated that students in the inquiry-based learning environment demonstrated higher levels of higher-order thinking skills compared to those in traditional settings. These findings suggest that the systematic implementation of inquiry-based strategies plays a critical role in enhancing higher-order cognitive processes. This study contributes to the existing literature by providing comparative empirical evidence on the effectiveness of inquiry-based learning in promoting higher-order thinking skills and highlights the importance of teacher professional development in supporting its successful implementation.