Objective To investigate B1 cell and follicular helper T (Tfh) levels in children with systemic lupus erythematosus (SLE) and to assess whether mesenchymal stem cells (MSCs) regulate peripheral blood B1 cells and Tfh cells in pediatric SLE. Methods Peripheral blood mononuclear cells (PBMCs) were isolated from children with SLE and from controls. B1 and Tfh cells were measured, differences between groups were analyzed, and correlations with clinical indices were evaluated. Human umbilical cord mesenchymal stem cells (hUCMSCs) were co-cultured with PBMCs for 48 hours at hUCMSC:PBMC ratios of 1:10 and 1:20, with PBS-treated PBMCs as control; post-culture proportions of B1 and Tfh cells were re-assessed. Results hUCMSCs adhered to plastic with spindle-shaped morphology, showed robust growth, and exhibited osteogenic and adipogenic differentiation. B1 and Tfh cell levels were higher in children with SLE than in controls (P<0.05) and were not significantly correlated with serum complement, immunoglobulins, antibody levels, or SLE Disease Activity Index scores (P>0.05). Tfh cells showed a trend toward association with serum C4 and IgM. After co-culture, no statistically significant differences in B1 or Tfh cell proportions were detected among the PBS control and hUCMSC co-culture groups (P>0.05). Conclusions B1 cells and Tfh cells differ between children with SLE and controls and may be involved in SLE pathogenesis. hUCMSCs do not appear to exert therapeutic effects in SLE by regulating peripheral blood B1 and Tfh cell numbers.