Background <p>Urachal carcinoma (UrC) is a rare epithelial malignant tumor of the urinary system, with an age-standardized incidence of 0.32 per million population, accounting for 0.35–0.70% of all bladder tumors. Adenocarcinoma is the most common histological subtype of UrC, while squamous cell carcinoma is extremely rare, representing only 2% of all UrC cases, and is associated with a high mortality rate. Due to its occult onset and high malignancy, urachal squamous cell carcinoma (USC) is often diagnosed at an advanced stage, and current understanding of this disease remains limited. Herein, we report a rare case of USC with complete clinical and therapeutic records, with no evidence of recurrence or metastasis identified during a 4-year follow-up period to date. Additionally, exome sequencing was performed, revealing that the gene mutation pattern of the carcinoma cell is closer to that of gastrointestinal tumors.</p> Case presentation <p>A 58-year-old male presented to a local hospital twice with gross hematuria at a 6-month interval. No abnormalities were detected on cystoscopy, urinary exfoliative cytopathology, or pelvic magnetic resonance imaging (MRI). Five months after the second visit, the patient was referred to our hospital for the third episode of hematuria. Computed tomography urography (CTU) and pelvic MRI identified abnormal signals in the anterior wall of the urinary bladder, suggesting a urachal tumor. Subsequent cystoscopy with biopsy revealed acute and chronic mucosal inflammation with hemorrhage. The patient then underwent extended partial cystectomy combined with urachal and umbilical resection. Pathological examination confirmed moderately differentiated squamous cell carcinoma of the urachus, which had invaded the muscularis propria and lamina propria of the bladder wall. Exome sequencing was performed on DNA extracted from the patient’s tumor tissue, demonstrating that the tumor’s gene mutation pattern was closer to that of gastrointestinal tumors. Postoperatively, the patient received gemcitabine plus cisplatin chemotherapy, which was switched to docetaxel plus carboplatin adjuvant chemotherapy due to grade III myelosuppression. At the 4-year postoperative follow-up, no local or distant metastatic lesions have been identified, and long-term prognosis remains under surveillance.</p> Conclusions <p>This is a rare reported case of USC with long-term survival, accompanied by gene sequencing data. Most currently reported cases of USC are diagnosed at an advanced stage; thus, early diagnosis, complete surgical resection, and adjuvant chemoradiotherapy may contribute to long-term remission. In this patient, despite clear identification of the tumor on cross-sectional imaging, cystoscopic biopsy failed to retrieve tumor tissue, indicating that USC may not penetrate the bladder wall in a very early stage. We favor ultrasound-guided percutaneous biopsy may be a more appropriate diagnostic modality than cystoscopic biopsy in patients who present with small protrusions at the urachal-bladder junction and hematuria, in the absence of other imaging evidence of urinary tract tumors. Furthermore, gene sequencing results confirmed that USC is more similar to gastrointestinal tumors, which may originate from intestinal wall residues retained in the cloaca during embryonic development.</p>