Background: Fecal incontinence (FI) is a stressful condition for children and their parents that may affect the patient’s psychological well-being. Evaluating the patients’ psychological status may help physicians manage the disease effectively. Objectives: This study aimed to assess the emotional and behavioral disturbances in children with FI who were referred to the pediatric gastroenterology clinic in Mofid Children’s Hospital from April 2021 to 2022. Methods: This cross-sectional study included children (over four years old) with chronic constipation and fecal incontinence. The diagnosis of chronic constipation and FI were made according to Rome-IV criteria. The Child Behavior Checklist (CBCL) evaluated patients’ emotional, behavioral, and social problems. Results: One hundred one patients with a mean age of 7.96 years were enrolled in the study; 67.32% were males. According to CBCL, 12% (12 patients) indicated emotional and behavioral problems, with CBCL scores in the clinical or at-risk range. We detected anxious/depressed problems in five (4.95%), withdrawn/depressed problems in eight (7.92%), somatic complaints in seven (6.93%), social problems in eight (7.92%), thought problems in nine (8.91%), attention problems in seven (6.93%), rule-breaking behavior in two (1.98%), and aggressive behavior in nine (8.91%) patients. The risk of internalizing and externalizing disorders was reported in four (3.96%) and five (4.95%) patients. Also, eight (7.92%) and seven (6.93%) patients had clinical symptoms of internalizing and externalizing disorders, respectively. There was no significant relationship between patients’ age and gender with the CBCL scores in any subscales. However, there was a significant difference in the total score among the age groups (P = 0.04). Conclusions: The relatively high prevalence of emotional, behavioral, and social problems in our study corroborates the importance of psychological screening of children with FI during the treatment process.