Photosynthesis is an important yet a complex concept of school biology. Literature has identified numerous alternative conceptions of students about this aspect of Biology. Keeping in mind the importance of this aspect of life sciences this study aimed to examine grade 10 students’ conceptual understanding and alternative conceptions about photosynthesis with a view to compare it across school system and gender in the city of Gilgit. The study employed cross sectional survey design. A 20-item Conceptual Understanding about Photosynthesis (CUP) test was adopted for the study. The test encompassed six major aspects of photosynthesis (i.e. physiology, energy, biochemical, autotrophy, photosynthesis and respiration, ecology). CUP test was directly administered to randomly selected 204 grade 10 students from public (n =101) and private (n =103) schools of Gilgit. The selected sample represented male (n =102) and female (n = 102) students. Results of the study revealed that students’ overall conceptual understanding about photosynthesis was 53% of the total score (20). However, students’ performance in three aspects of photosynthesis (i.e. ecology, autotrophy, biochemical reaction) was higher than the overall score. Conversely, the students found rest of the three aspects (i.e. energy, photosynthesis and respiration, and physiology) relatively difficult. Furthermore, students from private schools outperformed their counterparts in public schools in overall conceptual understanding about photosynthesis (p<0.001) as well as in the aspects of biochemical (p<0.001), photosynthesis and respiration (p<0.001), and ecology (p<0.001). Moreover, score favored male students in the two aspects including energy (p<0.05) as well as photosynthesis and respiration (p<0.01). Results of the study would have implications for practice, policy and further research.