Introduction Although recent research has focused on the effects of maternal eating disorders (EDs) on children, little is known about the effect of maternal EDs on neurobiological outcomes in newborns and infants. This study is the first to investigate neurobehavioural regulation and cognitive development in newborns and infants of mothers with EDs. Methods Women with an active and past ED and healthy controls were recruited to a prospective longitudinal study during their first trimester or second trimester of pregnancy. Newborns and infants of mothers with ED were compared with newborns and infants of healthy controls on (a) neurobehavioural dysregulation using the Brazelton Neonatal Behavioural Assessment Scale at 8 days postpartum (active ED, n = 15; past ED, n = 20; healthy controls, n = 28); and (b) cognitive development using the Bayley Scales of Infant and Toddler Development at 1‐year postpartum (active ED, n = 18; past ED, n = 19; healthy controls, n = 28). In order to maintain the largest possible sample at each time point, sample size varied across time points. Results Newborns of mothers with an active ED had worse autonomic stability when compared with newborns of healthy controls [B = −0.34 (−1.81, −0.26)]. Infants of mothers with a past ED had poorer language [B = −0.33 (−13.6, −1.9)] and motor development [B = −0.32 (−18.4, −1.3)] compared with healthy controls. Conclusions Children of mothers with ED display neurobehavioural dysregulation early after birth and poorer language and motor development at 1 year. These characteristics suggest evidence of early neurobiological markers in children at risk. Differential outcomes in children of women with active versus past ED suggest that active symptomatology during pregnancy might have an effect on physiological reactivity while cognitive characteristics might be more stable markers of risk for ED.