Gender disparity in science and mathematics performance is being researched internationally. In a complex education system, like Pakistan, studying the difference in isolation may not generate holistic understanding. Therefore, this paper investigates changes in trends of performance in Science and Mathematics for both genders across public and private schools. Data were gathered from a nationwide sample of elementary grades students (n=15,391) using SATs/MATS. Independent t-test and two-way-ANOVA were employed to analyse data. Results revealed that girls outperformed boys in Science (p<0.01) while no gender differences in performance were observed in Mathematics. Gender and school systems demonstrated significant interaction effect only in mathematics, unveiling that girls perform better in public schools while this difference diminished in the private school system. The results show implications for employing gender-fair policies and practices in science and mathematics education.