Our previous study found that two novel cancer-related genes PRR11 and SKA2 constitute a classic gene pair that is regulated by p53 and NF-Y in lung cancer. However, their role and regulatory mechanism in breast cancer remain elusive. In this study, we found that the expression levels of PRR11 and SKA2 are upregulated and have a negative prognosis value in breast cancer. Loss-of-function experiments showed that RNAi-mediated knockdown of PRR11 and/or SKA2 inhibits proliferation, migration and invasion of breast cancer cells. Mechanistic experiments revealed that knockdown of PRR11 and/or SKA2 causes dysregulation of several downstream genes including CDK6, TPM3, USP12, etc. Luciferase reporter assay demonstrated that wild type p53 significantly represses the PRR11-SKA2 bidirectional promoter activity whereas not NF-Y. Intriguingly, NF-Y is only essential for and correlated with the expression of PRR11 but not SKA2. Consistently, adriamycin-induced (ADR) activation of endogenous p53 also causes significant repression of PRR11 and SKA2 gene pair expression. Notably, breast cancer patients with lower expression levels of either PRR11 or SKA2 along with wild type p53 exhibit better disease-free survival compared with others with p53 mutation and/or higher expression levels of either PRR11 or SKA2. Collectively, our study indicates that the PRR11 and SKA2 transcription unit might be an oncogenic contributor and serves as a novel diagnostic and therapeutic target in breast cancer.