MicroRNA‐96 (miR‐96) is a vertebrate conserved microRNA which plays important roles in various cancers including renal cell carcinoma (RCC). However, its function and mechanism in RCC are still unclear. In this study, miR‐96 was found to be downregulated in RCC based on The Cancer Genome Atlas datasets analyses, and its target genes, which predicted by TargetScan, were investigated. Among these target genes, neuronal pentraxin 2 (NPTX2) was upregulated more than 15‐fold in RCC, and moreover, closely related to patient survival. To validate its targeting of NPTX2 experimentally, reverse transcription polymerase chain reaction, Western blot analysis, and dual‐luciferase assays were performed, and results of these assays demonstrated that miR‐96 inhibited expression of NPTX2 through a single 3′‐untranslated region targeting site. Furthermore, transfection assays in RenCa and 786‐O cells showed miR‐96 and small interfering RNA of NPTX2 inhibited cell proliferation, migration, and invasion and overexpression of NPTX2 recovered the inhibition of miR‐96. In conclusion, the present study reveals a novel regulatory mechanism of miR‐96 on NPTX2 expression in RCC, and the potential of miR‐96 as a RCC tumor repressor deserves further investigation.