Objectives To examine the relationships between children's moderate-to-vigorous physical activity (MVPA), sedentary behaviours, and academic performance. Design This study investigated cross-sectional relationships between children's accelerometer-measured physical activity and sedentary behaviour patterns, and academic performance using a standardised, nationally-administered academic assessment. Methods A total of 285 Australian children aged 9–11 years from randomly selected schools undertook 7-day 24 h accelerometry to objectively determine their MVPA and sedentary behaviour. In the same year, they completed nationally-administered standardised academic testing (National Assessment Program—Literacy and Numeracy; NAPLAN). BMI was measured, and socio-demographic variables were collected in a parent-reported survey. Relationships between MVPA, sedentary behaviour and academic performance across five domains were examined using Generalised Linear Mixed Models, adjusted for a wide variety of socio-demographic variables. Results Higher academic performance was strongly and consistently related to higher sedentary time, with significant relationships seen across all five academic domains (range F = 4.13, p = 0.04 through to F = 18.65, p = <0.01). In contrast, higher academic performance was only related to higher MVPA in two academic domains (writing F = 5.28, p = 0.02, and numeracy F = 6.28, p = 0.01) and was not related to language, reading and spelling performance. Conclusions Findings highlight that sedentary behaviour can have positive relationships with non-physical outcomes. Positive relationships between MVPA and literacy and numeracy, as well as the well documented benefits for MVPA on physical and social health, suggest that it holds an important place in children's lives, both in and outside of school.