Crohn's disease is a recurrent, progressive, immune‐mediated inflammatory disease and merely manifests non‐specific symptoms at early stage. In this study, we isolated peripheral blood mononuclear cells (PBMCs) to determine whether PBMC miRNAs are reliable biomarkers for Crohn's disease diagnosing and monitoring. 5 Crohn's disease patients and 5 healthy controls were recruited to find differentially expressed miRNAs by next generation sequencing. Candidate PBMC miRNAs were further validated by qRT‐PCR in another cohort consisting of 86 Crohn's disease patients and 39 healthy controls. We found PBMC miR‐582‐5p could diagnose Crohn's disease with the area under receiver operating characteristic curve (AUROC) of 0.701(95%CI 0.606–0.796, p < .001). While PBMC miR‐96‐5p was significantly higher in active Crohn's disease and correlated with both clinical (ρ = 0.376, p < .001) and endoscopic activity (ρ = 0.512, p = .015). Furthermore, PBMC miR‐96‐5p had a better performance in recognizing active Crohn's disease with AUROC of 0.727 (95%CI 0.609–0.844, p = .001) than C‐reactive protein (CRP), erythrocyte sedimentation rate (ESR) and fecal calprotectin. In conclusion, PBMC miR‐582‐5p may be further utilized as a diagnostic biomarker, while miR‐96‐5p may be a novel and valuable biomarker in monitoring disease activity.