To investigate associations between motor skills, exercise capacity and cognitive functions, and evaluate how they correlate to academic performance in mathematics and reading comprehension using standardised, objective tests.This cross-sectional study included 423 Danish children (age: 9.29±0.35 years, 209 girls). Fine and gross motor skills were evaluated in a visuomotor accuracy-tracking task, and a whole-body coordination task, respectively. Exercise capacity was estimated from the Yo-Yo intermittent recovery level 1 children's test (YYIR1C). Selected tests from the Cambridge Neuropsychological Test Automated Battery (CANTAB) were used to assess different domains of cognitive functions, including sustained attention, spatial working memory, episodic and semantic memory, and processing speed. Linear mixed-effects models were used to investigate associations between these measures and the relationship with standard tests of academic performance in mathematics and reading comprehension.Both fine and gross motor skills were associated with better performance in all five tested cognitive domains (all P<0.001), whereas exercise capacity was only associated with better sustained attention (P<0.046) and spatial working memory (P<0.038). Fine and gross motor skills (all P<0.001), exercise capacity and cognitive functions such as working memory, episodic memory, sustained attention and processing speed were all associated with better performance in mathematics and reading comprehension.The data demonstrate that fine and gross motor skills are positively correlated with several aspects of cognitive functions and with academic performance in both mathematics and reading comprehension. Moreover, exercise capacity was associated with academic performance and performance in some cognitive domains. Future interventions should investigate associations between changes in motor skills, exercise capacity, cognitive functions, and academic performance to elucidate the causality of these associations.