Emotional and behavioral problems have been considered an indicative of mental disorder in children. Mental health problems affect 10-20% of children and adolescents living in low-income and middle-income countries. Evidence suggests that disruptions in the biological rhythm may be a primary cause of emotional and behavioral changes, which affects several psychological functions and moods. Thus, this study aimed at verifying the association between biological rhythm and emotional and behavioral problems in schoolchildren living in Southern Brazil. This is a cross-sectional study with a school-based sample conducted between August 2015 and November 2016. The presence of emotional and behavioral problems in children was verified by the Strengths and Difficulties Questionnaire (SDQ), parents' version. This is a 25-item assessment questionnaire used to screen mental health problems in children and adolescents (from 4 to 17 years of age) in the last 6 months. The Biological Rhythm Interview of Assessment in Neuropsychiatry-Kids (BRIAN-K) was used to measure the degree of biological rhythm disruption. The BRIAN-K consists of 20 items; from among these, 17 items are added to generate a quantitative measure, with greater scores indicating more biological rhythm disruption. The final score can also be divided into four subscales: sleep, social rhythm, eating pattern and overall activities. A total of 609 children responded to the assessment instruments. With regard to parents or primary caregiver, 596 completed the assessment and 13 (2%) were not located or refused to participate in the study. Thus, 596 dyads were included in the analysis. Children with emotional and behavioral problems presented higher scores in all domains of BRIAN-K: sleep, social, activity, eating pattern and total score (p < 0.001). The following variables remained associated with emotional and behavioral problems after adjusted analysis: BRIAN-K total score (p < 0.001) and all subscales sleep (p < 0.001), social (p < 0.001), activity (p < 0.001) and eating pattern (p < 0.001). Children with emotional and behavioral problems presented higher biological rhythm disruption when compared with children without emotional and behavioral problems. Our study emphasizes the importance of biological rhythm and its influence on emotional and behavioral problems in schoolchildren. Early detection of any biological rhythm disruption may enhance further assessment of any eventual emotional and behavioral problem and even a psychopathology.