In this study, we investigated the prognostic significance of the expression of N6-methyladenosine (m6A) RNA methylation regulatory genes in kidney renal papillary cell carcinoma (KIRP). RNA-sequencing data analysis showed that 14 of 20 major m6A RNA methylation regulatory genes were differentially expressed in the KIRP tissues from The Cancer Genome Atlas (TCGA) database. We constructed a prognostic risk signature with three m6A RNA methylation regulatory genes, IGF2BP3, KIAA1429 and HNRNPC, based on the results from univariate and LASSO Cox regression analyses. Multivariate Cox regression analysis confirmed that the risk score based on the three-gene prognostic risk signature was an independent predictive factor in KIRP. The overall survival of high-risk KIRP patients was significantly shorter than the low-risk KIRP patients. Expression of the three prognostic risk-related genes correlated with the AJCC and TNM stages of KIRP patients from TCGA and GEPIA datasets. ROC curve analysis showed that the three-gene prognostic risk signature precisely predicted the 1-year, 3-year and 5-year survival of KIRP patients. These findings demonstrate that expression of three prognostic risk-related m6A RNA methylation regulatory genes accurately predicts survival outcomes in KIRP patients.