Differences in students' Mathematics achievement are accounted by many factors of which gender and school system are two contributing variables. This study aimed to explore the differences in grade 10 students' Mathematics achievement across gender and school systems (public and private) in Skardu, Gilgit-Baltistan. The study sample comprised 356 grade 10 students selected through stratified random sampling. Of these, 165 students were from public and the remaining191 students were enrolled in private schools. The sample represented boys (it = 187) and girls (n = 169). A cross-sectional survey was employed and data collected through a newly developed and validated Mathematics Achievement Test (MAT). Data were analysed using the non-parametric equivalence of the independent t-test. Results showed that students' overall score in MAT was 31.5%. Furthermore, students' performed slightly better in MCQs than CRQs. Of the four content domains in MAT, information handling was the easiest. Furthermore, students' performed better in the knowledge domain as compared to the application and reasoning domains but the difference was not significant. Gender comparison of MAT overall scores revealed girls' better performance than boys but the difference was not significant (p > 0.05). Likewise, gender comparison indicated no significant differences for students' scores in MCQs and CRQs, content domains and cognitive domains (p > 0.05 for all). Within school comparison exhibited no significant gender differences in the overall performance of both public and private schools. However, within public schools girls performed significantly better in numbers & operations, algebra (p < 0.01) and lower level of cognition i.e. knowledge (p < 0.05). Nevertheless, within private schools no significant gender difference was observed in any category of MAT. However, comparison of school systems revealed significantly better performance of private schools to public schools in all categories of MAT. This study provides insights into differences in students' Mathematics performance in relation to their gender and the schools attended. It provided information about students' knowledge in various content and cognitive domains of Mathematics for policy and practice. This study can be replicated nationally using MAT. A qualitative aspect can be added to explore the reasons for students' performances in Mathematics.