Objective: To investigate the differential expression profile of urinary exosomal microRNA (miRNA) in patients with mesangial proliferative glomerulonephritis (MsPGN) and healthy controls and their potential role in the pathogenesis of MsPGN. Methods: Urine specimens were collected from five MsPGN patients and five healthy controls, and differentially expressed miRNAs were screened using high-throughput sequencing technology. The sequenced urinary exosomal miRNAs were further investigated by quantitative real-time polymerase chain reaction (qRT-PCR) in a validation cohort (16 MsPGN patients and 16 healthy controls). Correlation and receiver operating characteristic (ROC) curve analyses were used to determine the association between clinical features and miRNA expression in MsPGN. Finally, fluorescence in situ hybridization was performed to detect miRNA expression in the renal tissues of MsPGN patients. Results: Five differentially expressed miRNAs (miR-125b-2-3p, miR-205-5p, let-7b-3p, miR-1262, and miR-548o-3p) were identified by qRT-PCR. The expression of these miRNAs correlated with ACR, 24hUpro, mAlb, UA, and combined yielded a ROC curve area of 0.916 in discriminating MsPGN patients from the controls. In addition, the expression of miR-205-5p, let-7b-3p, miR-1262, and miR-548o-3p was elevated in the MsPGN patient group, and miR-125b-2-3p was decreased in the MsPGN patient group. Conclusions: Differential expression of urinary exosomal miRNAs may pose a risk of MsPGN and help distinguish MsPGN patients from controls. Certain miRNA expressions may be associated with disease progression, contributing to the epigenetic understanding of the pathophysiology of MsPGN.