Background: Functional constipation (FC) is a common issue in pediatric healthcare, causing significant physical and emotional distress for patients and their families. Objectives: This study aimed to investigate the prevalence of behavioral issues in children diagnosed with functional constipation, exploring their characteristics and relationship with various factors. Methods: We conducted a case-control study involving 107 children and adolescents (aged 2 to 18 years) with chronic functional constipation as the case group and 107 children without this condition as the control group. The Strengths and Difficulties Questionnaire (SDQ) was employed to evaluate different aspects of behavioral patterns. Results: The comparison of various behavioral components assessed by the SDQ between the case and control groups revealed significantly higher average scores for emotional symptoms (0.85 ± 0.81 vs. 0.55 ± 1.03, P = 0.019), peer relationship problems (1.76 ± 2.23 vs. 0.76 ± 1.18, P = 0.001), and prosocial behavior (8.12 ± 1.87 vs. 7.42 ± 1.64, P = 0.002) in children with chronic functional constipation. Within the chronic constipation group, peer relationship issues were more common in boys, whereas girls exhibited more problems with prosocial behavior. Moreover, issues related to hyperactivity/inattention and prosocial behavior were more frequent in older children with chronic constipation. Conclusions: Chronic functional constipation in children is strongly associated with behavioral changes and problems, which are influenced by the demographic and anthropometric features of the patients.