Human Pinx1 protein, associated with shelterin proteins, is widely revealed as a haploinsufficient tumor suppressor. Growing evidence has manifested the deregulation of PinX1 in distinct cancers. Nonetheless, the loss status of PinX1 and its diagnostic, prognostic and clinicopathological significance in Basal-like breast cancer are still unclear. In the present study, the PinX1 expression levels of breast cancer tissues were investigated by qRT-PCR and immunoblotting assays. Then immunohistochemistry (IHC) was performed to detect PinX1 expression on a tissue microarray. The optimal threshold for PinX1 positivity was determined by receiver operating characteristic (ROC) curve analysis. To clarify the probable role of PinX1 in BLBC, the PinX1 knockout and stably over-expressed MDA-MB-231 cell lines were constructed by the CRISPR-Cas9 system and gene transfection. The association of PinX1 expression with cell proliferation, migration and apoptosis of MDA-MB-231 cells were observed by CCK-8 assay, wound healing assay, transwell assay, flow cytometric analysis and immunoblotting of the cleaved caspase-3 protein level. Our results showed that both PinX1 mRNA and protein expression were downregulated in breast cancer tissues (P<0.05). In IHC analysis, the optimal cut-off parameter for PinX1 positive expression was 62.5% (the AUC was 0.749, P<0.01). PinX1 positivity was 76.9% (10/14) in luminal subtypes, 50% (5/10) in Her2-enriched breast cancer and 27.3% (9/33) in basal-like subtypes. Besides, in 59 invasive ductal breast carcinomas, PinX1 expression was inversely related to histology grade (P<0.05) while it was positively associated with PR status (P<0.05) and ER status (P<0.05). These results indicated that low expression of PinX1 correlated with aggressive clinicopathological significance of breast cancer, especially in the basal-like subtype. Besides, we identified that overexpression of PinX1 inhibited the proliferation rates and migration ability and increased the apoptosis rates of BLBC. Our findings demonstrated that low expression of PinX1 was associated with malignant behaviors in basal-like subtype of breast cancer. PinX1 is likely a feasible biomarker and molecular target of BLBC.