Capsule endoscopy (CE) may be used for the evaluation and follow-up of patients with Crohn’s disease. CE scores correspond to the degree of mucosal inflammation, a major therapeutic target. The aim of this meta-analysis and systematic review was to determine whether mucosal healing assessment by CE may serve as a predictor of clinical remission in patients with Crohn’s disease. To identify observational or controlled English-language full-text studies assessing mucosal healing by CE in patients with Crohn’s disease up to 30 September 2016, we searched PubMed, Embase, Central, Medline, and Scopus using the key words ‘mucosal healing’ and ‘capsule endoscopy’. A meta-analysis was carried out using ‘Comprehensive meta-analysis’ software. Pooled odds ratios and 95% confidence intervals were calculated. Five observational studies including 142 patients from five countries fulfilled the inclusion criteria. No publication bias was found by funnel plot. The mucosal healing CE score was found to be significantly associated with improved outcome after a follow-up of 12 weeks to 24 months, with an odds ratio of 11.06 (95% confidence interval: 3.74–32.73, P<0.001). The degree of heterogeneity among the studies was small (Q=2.014, d.f.[Q]=3, P=0.569 and I2=0). Endoscopy scores may play a role in the long-term prognostic evaluation of patients with Crohn’s disease. Our results may be accepted as proof of concept, but larger studies are needed to corroborate these findings.