Urinary tract infection (UTI) is the most common bacterial infection encountered in kidney transplant recipients. Graft pyelonephritis (GPN) is associated with acute kidney injury and renal allograft scarring. However, the influence of GPN on renal allograft outcome in kidney transplant recipients remains controversial. Two hundred sixty-five kidney transplant recipients were evaluated for the impact of early-onset GPN on renal allograft functions between January 2001 and December 2011. Early-onset GPN was defined as the first GPN episode occurring within 6 months after kidney transplantation. Thirty recipients (11.3%) were diagnosed with early-onset GPN. During the mean follow-up period of 69.1 ± 28.9 months, 56 (21.1%) recipients showed renal allograft outcomes of a > 30% reduction in the estimated glomerular filtration rate (eGFR) over 2 years. The poor outcome was significantly more frequent in the early-onset GPN group (13 patients; 43.3%) than in those without early-onset GPN (43 patients; 18.3%) (P = 0.002). Moreover, the linear mixed model revealed a significant difference in the eGFR decline rate over time between the two groups (P < 0.001). Kaplan-Meier analysis showed that renal allograft event-free survival was significantly lower in the early-onset GPN group (P = 0.006). Multivariate Cox regression analyses revealed that early-onset GPN was independently predictive of poor renal allograft outcomes (hazard ratio, 1.96; 95% confidence interval, 1.02-3.77; P = 0.04). In conclusion, early-onset GPN is independently associated with impaired renal functions in kidney transplant recipients. Thus, early-onset GPN could be a predictor for long-term outcome of renal allografts.