Paediatric systemic lupus erythematosus (pSLE) refers to childhood-onset systemic lupus erythematosus. pSLE has its own unique characteristics, and its pathogenesis is unclear. To study the relationship between microRNAs (miRNAs) and pSLE, we selected three pSLE patients who were newly diagnosed and had not yet been treated, and two controls were also included. We collected their peripheral blood mononuclear cells to perform Agilent human miRNA (8×15 k) 12.0 analysis. To verify the results, we next selected 12 other pSLE patients who had different disease activities and 3 healthy controls and conducted real-time PCR. The results showed high expression of miRNA-516a-3p, miRNA-629 and miRNA-525-5p in pSLE patients with active disease; these levels were normal in patients without active disease. Increased expression levels of these three miRNAs were positively correlated with the score obtained from the systemic lupus erythematosus disease activity index scoring system (SLEDAI) 2000 and C-reactive protein (CRP) levels. Furthermore, the target genes of these three miRNAs were important to the pathogenesis of pSLE. Therefore, these three miRNAs might be specific to pSLE and may be used as novel biomarkers of pSLE to diagnose and monitor the disease.