Cultivating students’ enjoyment of science is one of the significant aims of science education. However, it seems challenging to achieve this goal in most countries or economies. Using the Trends in International Mathematics and Science Study (TIMSS) 2019 Hong Kong data, this study aims to identify multiple configurations of school conditions to develop students’ science enjoyment with a School Analytics model. A fuzzy-set Qualitative Comparative Analysis (fsQCA) was employed to capture the potential asymmetric relationships and measure multiple combinations of different conditions. Results indicated that no single school condition was necessary or sufficient for high enjoyment of science (ES). While lacking instructional clarity was a sufficient condition for low enjoyment of science (∼ES). Three different configurations resulted in ES and ∼ES respectively. The combination of supportive school discipline and high instructional clarity jointly constituted a crucial science learning environment for developing science enjoyment in Hong Kong secondary schools. Under this environment, the effectiveness of science investigation was further discussed to enhance science enjoyment. Our study enlightens educational practitioners to improve students’ science enjoyment with multiple combinations of school conditions.