Relational reasoning, the ability to detect meaningful patterns, matures through adolescence. The unique contributions of verbal analogical and nonverbal matrix relational reasoning to science and maths are not well understood. Functional magnetic resonance imaging data were collected during science and maths problem-solving, and participants (N = 36, 11-15 years) also completed relational reasoning and executive function tasks. Higher verbal analogical reasoning associated with higher accuracy and faster reaction times in science and maths, and higher activation in the left anterior temporal cortex during maths problem-solving. Higher nonverbal matrix reasoning associated with higher science accuracy, higher science activation in regions across the brain, and lower maths activation in the right middle temporal gyrus. Science associations mostly remained significant when individual differences in executive functions and verbal IQ were taken into account, while maths associations typically did not. The findings indicate the potential importance of supporting relational reasoning in adolescent science and maths learning.