Background Nephrogenic adenoma (NA) is an epithelial lesion that usually occurs in the mucosa of the urinary tract. Rare cases of deep infiltrative or perinephric lesions have also been reported. Recently, NA with characteristic fibromyxoid stroma (fibromyxoid NA) has been proposed as a distinct variant. Although shedding of distal renal tubular cells due to urinary tract disorder has been postulated as the cause of NA in general, the mechanism underlying extraurinary presentation of NA and fibromyxoid stromal change in fibromyxoid NA remains unknown.Case presentation: An 82-year-old man had distal ureteral carcinoma and underwent total nephroureterectomy. The patient had no prior history of urinary tract injury or radiation. Periodic acid-Schiff staining-positive eosinophilic deposits were seen in the periureteral and perinephric regions proximal to the ureteral carcinoma. The eosinophilic structureless deposits in the stroma of fibromyxoid NA were microdissected and subjected to liquid chromatography/mass spectrometry (LC/MS). The analysis revealed the presence of a substantial amount of uromodulin (Tamm–Horsfall protein).The presence of urinary content in the stroma of perinephric fibromyxoid NA suggests that urinary tract failure and engraftment of renal tubular epithelial cells directly cause the lesion.Conclusions In conclusion, we reported a rare case of perinephric fibromyxoid NA with uromodulin deposits. In this study, proteomics analysis suggested the involvement of urinary material leakage. Mass spectrometry may be most effective when performed in lesions showing a characteristic morphology, especially in the stroma.