MicroRNAs (miRNAs) are a class of short non-coding RNA that can specially bind to the 3'-untranslated region of target mRNAs and regulate gene expression at the posttranscriptional level. This study investigated the effects of a miRNA binding site polymorphism (rs1051296) in solute carrier family 19, member 1 (SLC19A1) on serum methotrexate (MTX) concentrations in Chinese children with acute lymphoblastic leukemia (ALL). Genotyping for SLC19A1 rs1051296 G>T in 131 children with ALL was performed using the Sequenom MassArray system. A total of 131 patients received high-dose MTX treatment, and serum MTX concentrations were measured by a fluorescence polarization immunoassay 24 (MTX C24h) and 42 h (MTX C42h) after administration. The frequency of the rs1051296 T allele observed in this study (46.2 %) was significantly lower than that previously observed in a European population (60.7 %, P = 0.002). There was significant association between rs1051296 G>T and MTX C24h (29.97, 32.34, and 39.01 µmol/L for GG, GT, and TT genotypes, respectively, P = 0.04). The percentage of patients with an MTX concentration above the therapeutic threshold (40 μmol/L) was significantly lower in GG carriers compared with that in GT and TT carriers (8.6 % for GG genotype vs. 26.8 and 40.0 % for CT and TT genotypes, respectively, P = 0.02). Delayed elimination of MTX (C42h > 1 μmol/L) was less frequent in GG carriers than in GT and TT carriers. Rs1051296 G>T was associated with MTX plasma concentration, suggesting that miRNAs might be involved in the post-transcriptional regulation of SLC19A1.