Primary paraganglioma and small cell neuroendocrine carcinoma of the urinary bladder are rare tumors, comprising 0.05% of all bladder tumors and <1% of all malignant bladder tumors, respectively. These tumors can be the cause of a diagnostic dilemma or misdiagnosis on morphology. Paraganglioma is often mistaken for urothelial carcinoma and small cell carcinoma for poorly differentiated carcinoma or lymphoma. Herein, we report a case of primary paraganglioma and another of a small cell carcinoma of the urinary bladder and discuss their closest differential diagnoses. The diagnostic pitfalls should be kept in mind so that correct, timely diagnosis of these entities can be made due to implications in the management and prognosis.