Aim Although Cognitive behavioural therapy (CBT) potentially holds efficacy in addressing functional abdominal pain disorders (FAPDs) amongst children and adolescents, the persistent efficacy is uncertain. Methods We searched three databases to identify related randomized controlled trials (RCTs). Meta-analysis was performed using RevMan and Stata. Subgroup analyses were mainly conducted based on follow-up time. The GRADE approach was used to evaluate the certainty of the evidence. Results A total of 14 RCTs evaluating 858 patients were included. All RCTs were rated as having a high risk of bias. Compared with control groups, CBT was associated with improvement of general functional impairment (standardized mean difference (SMD) = -0.77, 95% CI [-1.12, −0.42], p < 0.05), higher treatment success (relative risk (RR) = 2.35, 95% CI [1.50, 3.69], p < 0.05), improvement of abdominal pain symptoms (SMD = −0.48, 95% CI [-0.73, −0.23], p < 0.05), QoL (SMD = 0.42, 95% CI [0.20, 0.64], p < 0.05), and psychological states (SMD = −0.95, 95% CI [-1.62, −0.27], p < 0.05). Conclusion This meta-analysis provides low to moderate quality evidence that CBT could significantly improve clinical outcomes and QoL for children and adolescents with FAPDs with improvement persisting until short-term follow-up. However, there were discrepancies regarding CBT's effects at mid- and long-term follow-up across different outcomes. More high-quality and longer-duration studies are thus warranted to explore the effectiveness of CBT in the future. Systematic review registration on prospero CRD42022369353.