Intolerance of uncertainty (IU) is the tendency to react negatively on affective, cognitive and behavioural levels to uncertain situations and to harbour negative beliefs about the implications of uncertainty. IU has been linked to psychopathology and shown to impact treatment outcomes. This study systematically reviewed the literature and performed a meta-analysis of the effects of psychotherapy on IU. A total of 22 studies (1491 participants) were identified in online searches and included in the meta-analyses. Analyses were performed on studies with passive and active control conditions. The pooled effect on IU from studies with passive control was large (g = −0.94 [95% CI −1.25 to −0.62]) but with significant heterogeneity. Pooled effects on IU from studies with active controls were not significant. Moderator analysis showed that among studies with a passive control condition, studies that recruited participants from clinical care facilities produced smaller effect sizes. Among studies with an active control condition, study quality significantly moderated the results, with higher quality leading to a larger effect size. These results indicate that changes in IU may be difficult to reliably achieve in psychotherapy and leave many questions about the effect of psychotherapy on IU unanswered, such as what active components produced the observed changes in studies with passive control.