Rationale:Male secretory breast cancer is a rare, low-grade carcinoma, especially in boys. Due to its rarity, not much is known about this disease.Patient concerns:A 5-year-old boy presented with a 1.4 cm painless mass in the right breast.Diagnoses:Ultrasonography could not distinguish whether the breast tumor was benign or malignant. After a biopsy of the lumpectomy specimen, it was diagnosed to be secretory breast carcinoma.Interventions:The patient underwent a modified radical mastectomy for his right breast. No postoperative chemotherapy or radiotherapy was performed. Next-generation sequencing of 211 cancer-related genes was detected, and the results revealed an ETV6-NTRK3 translocation and a PDGFRB c.2632A > G mutation. None of the most commonly altered molecules in male aggressive breast cancer (such as BRCA1-2, TP53, RAD51C, and RAD51D mutations) has been identified.Outcomes:The patient was still free from local recurrence or metastases at 6-month follow-up.Lessons:The genomic profile of male pediatric SCB is relatively simple, no other known driver genes have been found except for the ETV6-NTRK3 fusion. Our report will improve our understanding of secretory breast cancer.