Purpose of the study: This study aimed to investigate the effect of a Scientific Approach assisted by the Flying Water Apparatus on students’ analytical skills in projectile motion learning, specifically examining whether integrating inquiry-oriented activities with a physical visualization tool could effectively enhance students’ analytical thinking abilities. Methodology: This study employed a quasi-experimental design using a non-equivalent control group design. Participants consisted of Grade 10 science students at Madrasah Aliyah Universitas Islam Negeri Syarif Hidayatullah Jakarta selected through purposive sampling. Data were collected using an analytical skills test and a Student Response Questionnaire. Statistical analyses included Shapiro–Wilk normality tests, Levene’s and Bartlett’s homogeneity tests, Mann–Whitney U tests, independent-samples t-tests, and N-gain analysis. Main Findings: The experimental group achieved a higher posttest mean score (6.21) than the control group (4.57). Statistical analysis revealed a significant difference between groups (p = 0.001). The experimental group obtained a medium N-gain score (0.60), while the control group achieved a low N-gain score (0.23). The findings indicate that the scientific approach assisted by the Flying Water Apparatus significantly improved students’ analytical skills in projectile motion learning. Novelty/Originality of this study: This study integrates the Scientific Approach and a low-cost Flying Water Apparatus within a single instructional intervention to enhance analytical skills in projectile motion learning. Unlike previous studies that focused on conceptual understanding or learning achievement, this research specifically examines analytical skills based on the dimensions of differentiating, organizing, and attributing, thereby extending evidence regarding inquiry-based physics instruction and higher-order thinking development.