Research on active learning that emphasises question formulation activities has received less attention. This study was conducted to address the said gap identified in the literature by testing the thinking empowerment by questioning (TEQ) strategy on the level of conceptual understanding (CK) and critical thinking (CT) of students in Biology subjects. We used a pre-test-post-test non-equivalent control group design with a sample of junior high school students (n = 176). Participants were divided into three groups, namely (1) the TEQ group, 61 students; (2) PS (problem-solving) group, 60 students; and (3) the CS (conventional strategy) group, 55 students. We also considered the effect of school type (public and religious) on student performance in each treatment group and identified a potential correlation between CK and CT. Statistical results showed that TEQ had a more effective and significant effect on students' CK and CT than in the two control groups. However, we identified no difference between students in public and religious schools in each treatment group. In addition, this study also found a strong correlation between CK and CT through the implementation of TEQ. Finally, TEQ is an effective active learning strategy that promotes students' critical thinking in science content and is equally effective when administered to public and religious schools.