Healthy sleep is defined by the combination of adequate duration, good quality, and regular timing. In children, sleep thus depends on the interplay of individual, parental, organizational, community, and social variables, but only a few studies have addressed this issue in a comprehensive way nationwide. Using the Uruguayan nationally representative survey (Nutrition, Child Development, and Health Survey, Encuesta de Nutrición, Desarrollo Infantil y Salud, ENDIS), we present the first epidemiological characterization of chronobiological and sleep parameters in Latin American children. On average, Uruguayan urban children (n = 2437; 5− 10-years old) showed quite late chronotypes (MSFsc = 03:53 ± 1:07), moderate misalignment (SJL = 1.0 ± 0.9 h), and adequate sleep duration (SDweek = 9.9 ± 1.0 h). Further, we show the substantial influence of school shift schedules on children’s circadian typology and sleep patterns. Our results show that children attending the morning school shift have a higher risk of sleep problems than afternoon-school shift ones. The chronotype and sleep were earlier in morning-school shift children than in children attending the afternoon school shift. However, morning-school shift children had stronger misalignment, shorter sleep on school days, and a higher risk of chronic sleep deficit and non-healthy circadian misalignment (even worse in late chronotypes) than afternoonshift children. This evidence points to the need of evaluating policies to reorganize school start times to prevent the negative effects that early schooling seems to have on children’s sleep health, which has been neglected so far.