Purpose: To estimate associations between early motor abilities (at two age points, 7 and 18 months on average) and cognitive/language outcomes at age 3. To determine whether these associations are similar for children with and without positional plagiocephaly and/or brachycephaly (PPB).Methods: The Bayley Scales of Infant/Toddler Development 3 were given at all age points to 235 children with PPB and 167 without PPB. Linear regressions assessed longitudinal associations between fine and gross motor scales and cognition/language. Item analyses examined the contributions of specific motor skills.Results: Associations between 7-month motor skills and cognition/language were modest overall (effect sizes [ES] = − 0.08 to 0.10, p = .13 to .95). At 18 months, both fine and gross motor skills were associated with outcomes for children with PPB (ES = 0.21 to 0.41, p < .001 to .01), but among those without PPB, only fine motor skills were associated with outcomes (ES = 0.21 to 0.27, p < .001 to .001).Conclusions: Toddlers’ motor skills were associated with cognition and language at 3 years, particularly among children with PPB. Interventions targeting early motor development in infants and toddlers with PPB may have downstream benefits for other outcomes.