Lactobacillus plantarum IS-10506 is a novel probiotic isolated from Indonesian traditional fermented buffalo milk dadih. Probiotics are clinically proven to be effective in accelerating recovery after urinary tract infection (UTI) and in decreasing recurrent UTI in children with or without structural disorders of the urinary tract. This study aimed to investigate the role of the probiotic L. plantarum IS-10506 in activating and regenerating renal epithelial stem cells in pyelonephritic rats. Fifty-five 20-weeks-old male Sprague-Dawley rats were randomised into control, lipopolysaccharide (LPS) and treatment (LPS and probiotic) groups. Pyelonephritis was induced with Escherichia coli ATCC 25922 LPS administered via a urethral catheter on the first experimental day to the LPS and treatment groups. Microencapsulated L. plantarum IS-10506 was orally administered once daily for up to 14 days to the treatment group. On days 3, 5, 7, 10 and 14, five rats per group were sacrificed and their kidneys were immunohistochemically analysed for production of interleukin (IL)-10, lipocalin-2 and Ki-67 in the renal tubular cells. IL-10 production was upregulated starting from day 3 through day 14 in the treatment group (P<0.05) compared with that in the control and LPS groups. Moreover, treatment with the probiotic led to increased activation of renal tubular stem cell, as indicated by a higher lipocalin-2 production, and further proliferation of renal tubular stem cells was documented by a higher Ki-67 production. Taken together, these results indicate that the anti-inflammatory probiotic L. plantarum IS-10506 improves renal injury in pyelonephritic rats by activating endogenous renal tubular stem cells to proliferate into mature renal tubular epithelial cells.