Severe hand, foot, and mouth disease (HFMD) is sometimes associated with critical complications that can cause substantial child mortality. Activity of the vitamin D receptor (VDR) may influence the outcomes of enterovirus 71 (EV71) infection. This case‐control study aimed to assess the association of single‐nucleotide polymorphisms (SNPs) in the gene encoding the VDR with the severity of EV71‐associated HFMD. We selected four VDR SNPs based on linkage disequilibrium and functional prediction, and we tested them using the SNPscan multiple SNP typing method for potential association with severity of EV71‐associated HFMD. We found a significant association in the case of rs11574129 (G vs A: odds ratio (OR), 0.3439; 95% confidence intervals (CI), 0.1778‐0.6653) and rs739837 (T vs G: OR, 0.5580; 95%CI, 0.3352‐0.9291). Our results suggest that these two SNPs may influence the severity of EV71‐associated HFMD.