Research findings indicate a decline in students' motivation towards science learning through grade levels. However, there is a lack of studies investigating students' motivation comparing learning between science subjects and at different school levels. Using self-determination theory as a framework, this study compares perceived changes in intrinsic motivation and student opinions on the relevance of learning science themes among students in grades 6 and 9 (the end of compulsory schooling). To explore such learning, a multidimensional validated instrument is developed and used to collect empirical data from 2673 grade 6 students and 848 grade 9 students. Results from this research indicate statistically significant subject differences regarding sub-components of intrinsic motivation and a declining trend in students' opinions on the sub-scales of relevance for learning science themes with age. The results further indicate that grade 6 students report significantly higher science-related intrinsic motivation compared with grade 9 students. Suggestions and implications for practice and the potential impact on PISA science studies are discussed.