The study identified the cognitive mechanisms that underly individual differences in mathematics and reading. There is little systematic evidence regarding the connections between cognitive capabilities, mathematics and reading among high-school students with typical development. Moreover, the study aimed to examine whether or not gender is important in predicting cognitive capabilities and performance in mathematics and in reading. Structural equation modelling was used to examine the effects of gender, visuo-spatial working memory (VSWM), numerical working memory (NWM), verbal working memory (VWM), and visual processing (VP) on mathematics and reading performance. A sample of 190 students completed mathematics, reading, VSWM, NWM, VWM, and VP tests. Results showed that mathematical performance was influenced by NWM, VSWM, and VP, while VWM was found to be unrelated to such performance. On the other hand, VWM and VP, but not VSWM, predicted reading performance. Furthermore, while direct correlations between gender, NWM and VP were found, VWM and VSWM were not. The results are important for their theoretical and educational implications.