Background: Understanding how or whether sedentary behavior affects motor competence in young children is important considering that children spend a lot of time sedentary. The aim of this study was to examine whether sedentary behavior predicts motor competence in young children. Methods: A longitudinal study with a total of 372 children aged 3.5 years at baseline and 5 years at follow-up was conducted. Objectively measured activity patterns (i.e., using accelerometers) were conducted in a subsample with 188 children. Sedentary behavior was assessed both objectively and subjectively (parent-reported screen time). Locomotor and object control skill scores were determined using the Test of Gross Motor Development--Second Edition. A multivariable analysis was executed adjusting for potential confounders (such as age, sex, time spent in moderate- to vigorous-intensity physical activity, monitor wear time, body mass index z scores, and maternal education). Results: Sedentary behavior at either time point was not significantly associated with either locomotor or object control skills after adjusting for potential confounders. Discussion: Our results did not support the assumption that sedentary behavior affects motor competence in young children. Regardless, given the lack of consistency in the evidence base, we recommend to parents, educators, and health professionals that sedentary activities should be kept within government recommendations due to potential negative effects on child development.