Background: The aim of the present study was to investigate the potential predictive significance of pretreatment prognostic nutritional index (PNI) in patients with intravenous immunoglobulin (IVIG) resistant Kawasaki disease (KD). Methods: From June 2013 to May 2020, 1,257 eligible patients with KD were included in the present study. The pretreatment PNI was calculated as albumin level (g/L) +5×total lymphocyte count (109/L). The optimal cut-off values for PNI, neutrophil to lymphocyte ratio (NLR), and platelet to lymphocyte ratio (PLR) were evaluated via a receiver operating curve analysis. The impact of pretreatment PNI, NLR and PLR for IVIG resistant KD were tested with the Student’s t test or Mann-Whitney U test, and univariate and multivariate analyses. Results: The optimal cut-off values were identified as 49.50 for PNI, 3.58 for NLR and 164.00 for PLR, respectively. Lower pretreatment PNI levels were demonstrated to be associated with lower age, serum sodium levels and platelet counts, and with a higher incidence of IVIG resistance and higher C-reactive protein levels. There was a significantly negative association between the PNI and NLR, and PLR. In the logistic analyses, PNI as independent predictive factors were significantly correlated with IVIG resistance. The discriminatory ability of PNI was not inferior to NLR and PLR for predicting IVIG resistance. Conclusion: Pretreatment PNI could serve as a novel surrogate independent predictor for patients with IVIG resistant KD.