There is widespread interest in temperament and its impact upon cognitive and academic outcomes. Parents adjust their parenting according to their child’s temperament, however, few studies have accounted for parenting while estimating the association between temperament and academic outcomes. We examined the associations between temperament (2–3 years) and cognitive and academic outcomes (6–7 years) when mediation by parenting practices (4–5 years) was held constant, by estimating the controlled direct effect. Participants were from the Longitudinal Study of Australian Children (n = 5107). Cognitive abilities were measured by the Peabody Picture Vocabulary Test (verbal) and the Matrix Reasoning test (non-verbal). Literacy and numeracy were reported by teachers using the Academic Rating Scale. Mothers reported children’s temperament using the Short Temperament Scale for Toddlers (subscales: reactivity, approach, and persistence). Parenting practices included items about engagement in activities with children. Marginal structural models with inverse probability of treatment weights were used to estimate the controlled direct effect of temperament, when setting parenting to the mean. All temperament subscales were associated with cognitive abilities, with persistence showing the largest associations with verbal (PPVT; β = 0.58; 95%CI 0.27, 0.89) and non-verbal (Matrix Reasoning: β = 0.19; 0.02, 0.34) abilities. Higher persistence was associated with better literacy (β = 0.08; 0.03, 0.13) and numeracy (β = 0.08; 0.03, 0.13), and higher reactivity with lower literacy (β = -0.08; -0.11, -0.05) and numeracy (β = -0.07; -0.10, -0.04). There was little evidence that temperamental approach influenced literacy or numeracy. Overall, temperament had small associations with cognitive and academic outcomes after accounting for parenting and confounders.