Given the ubiquity of media use, especially among young children, the current study examines the impact of problematic media use (PMU) on children's (N = 418, M age = 53.62 months, SD = 3.38 months, M and SD are taken from the full sample of 418 children) physiological functioning. With previous studies reporting relations between media use, temperament, and physiological regulation, it was hypothesized that children with greater levels of PMU would have lower levels of baseline respiratory sinus arrhythmia (RSA; a measure of physiological regulatory capacity). It is further hypothesized that, higher levels of negative affect, and lower levels of effortful control (two distinct domains of temperament) would be linked to both PMU and RSA and that temperament might mediate the associations between PMU and physiological regulation (RSA) (i.e., higher negative affect, lower effortful control linked to higher PMU and lower RSA). Data were drawn from Wave 5 of Project M.E.D.I.A, a longitudinal study of the effects of media on children's development. Findings revealed that PMU was significantly linked to lower baseline RSA for girls, but not for boys. Both boys' and girls' PMU was linked to higher levels of negative affect. Girls' PMU was linked to lower effortful control. The hypothesis that temperament would meditate links between PMU and RSA was not supported. The sex difference in the relation between PMU and baseline RSA are discussed, including potential differences in content of media girls are using as well as potential developmental differences for girls' reactivity compared to boys. Overall, PMU may lead to diminished physiological regulation, especially for girls, and appears to be linked to higher levels of negative affect in children. It is important for parents to be aware of the potential impact media use may have on their children's development.