This study aimed to explore the influence of emotional factors on the efficacy and prognosis of endoscopic treatment in children with functional abdominal pain (FAP), and to identify related risk factors. A total of 66 children with FAP treated with endoscopy from January 2018 to June 2024 were evaluated using the Child Depression Scale, Child Anxiety Scale, Quality of Life Scale, and visual analog scoring. Patients' demographics, clinical symptoms, treatment methods, and outcomes were recorded. Symptom remission, recurrence rates, and quality of life changes were compared after 6 months. Pearson correlation and logistic regression analyses were conducted. High-anxiety (35 cases) and low-anxiety (31 cases) groups had mean pain scores of 4.85 ± 1.21 and 2.10 ± 0.85, respectively (P = .002). Recurrence rates were 34.3% and 9.7%, respectively (P = .012). Good-mood (20 cases) and bad-mood (46 cases) groups had quality of life scores of 85.50 ± 5.50 and 63.50 ± 7.00 (P <
.05). High-depression (25 cases) and low-depression (41 cases) groups had mean pain scores of 5.10 ± 1.10 and 2.40 ± 0.75 (P <
.05), with recurrence rates of 36.0% and 14.6%, respectively (P = .009). Anxiety and depression were positively correlated with pain scores (r = 0.60, r = 0.58, P <
.05) and negatively correlated with quality of life (r = -0.56, r = -0.54, P <
.05). Anxiety (OR = 3.20, P = .003) and depression (OR = 2.80, P = .007) were independent risk factors for recurrence. Emotional factors significantly affect the efficacy and prognosis of endoscopic treatment in children with FAP. Negative emotions increase recurrence risk and reduce treatment efficacy and quality of life. Psychological intervention should be considered to improve outcomes.