Objective To investigate the expression of heparinase (HPA) and miRNAs that may regulate HPA expression in the gastric cancer tissue. Methods The expression levels of HPA were determined by real-time PCR in the gastric cancer tissues. Based on the binding of miRNAs with the 3′ untranslated region (3′-UTR) of HPA, we screened for miRNAs targeting HPA using bioinformatics method and determined the expression levels of these miRNAs in the gastric cancer tissues using real-time PCR. Results The expression of HPA was higher in the gastric cancer tissues compared with those in the tumor-adjacent and normal tissues. Bioinformatics analysis showed that miR-18b,miR-137,miR-502,and miR-299-3p might inhibit HPA expression by binding to its 3′-UTR. Real-time PCR analysis revealed lower expression levels of miR-18b,miR-137,miR-502,and miR-299-3p in the gastric cancer tissues compared with in the adjacent and normal tissues. Conclusion HPA is highly expressed in the gastric cancer tissues; miR-18b, miR-137, miR-502 and miR-299-3p, which may target HPA, are lowly expressed, indicating miRNAs targeting HPA may participate in the carcinogenesis of gastric cancer.