Background Regional lymph node and distant metastasis are the most radical causes of high mortality in penile squamous cell carcinoma (PSCC) patients. However, the available biomarkers and detailed mechanisms underlying the metastasis of PSCC remain elusive. Here, we detected that HOXD11 was upregulated in tumors, especially in metastatic lymph nodes, highlighting its role in the progression of PSCC. We aimed to further explore the clinical significance, biofunctions and specific mechanisms of HOXD11. Methods Twelve PSCC tumors, metastatic lymph nodes and corresponding normal tissue pairs were examined by an RNA-seq panel of HOX genes to explore progressive biomarkers. The expression of HOXD11 was detected by qPCR and western blotting in our newly established PSCC cell lines. The clinical relevance and outcomes of HOXD11 were further validated in a large cohort of 267 PSCC patients by immunohistochemistry. Functional experiments in vitro and subcutaneous xenograft and footpad metastatic models were conducted to investigate the of HOXD11. The targeting relationship and mechanisms between HOXD11, miR-138-5p and FN1 were demonstrated by dual luciferase reporter assays and chromatin immunoprecipitation. Results HOXD11 expression was upregulated in PSCC tissues, especially in metastatic lymph nodes. High HOXD11 expression was associated with aggressive features, such as advanced pN stages, extranodal extension, pelvic lymph node and distant metastasis, and predicted poor survival. Furthermore, knockdown of HOXD11 not only inhibited cell proliferation, invasion and tumor growth but also reduced the burden of metastatic lymph nodes. Besides, miR-138-5p and FN1 reversed HOXD11-mediated oncogenic capacity. Mechanistic studies indicated that HOXD11 was post-transcriptionally regulated by miR-138-5p, bound to the promoter regions of FN1 activating the FN1/MMP2/MMP9 pathway to decompose the extracellular matrix and promoted epithelial mesenchymal transition-like phenotype metastasis. Conclusions HOXD11 promotes PSCC progression, predicting advanced disease with poor outcomes. HOXD11 could be a promising prognostic biomarker and potential therapeutic target for PSCC.