Spindle cell thymomas are the most common spindle cell neoplasms of the anterior mediastinum. These tumors belong to the group of thymic epithelial neoplasms and are known for their wide histomorphologic spectrum. This histological heterogeneity is the reason why unequivocal diagnosis can be challenging, especially when dealing with small biopsy material. Conversely, less conventional patterns of the tumor may also pose significant diagnostic problems in resected material and the differential diagnosis often includes other spindle cell neoplasms that are known to arise in the mediastinal cavity. These can be of variable origin and may share overlapping pathological features with spindle cell thymoma. Since spindle cell thymomas are tumors that primarily affect the adult population and predominantly arise from the thymic gland in the anterior mediastinum, this review will focus on the differential diagnosis with other spindle cell neoplasms that share similar demographic characteristics and, for the most part, originate from the anterior mediastinal compartment. These include other epithelial spindle cell tumors of thymic origin (sarcomatoid thymic carcinoma and spindle cell carcinoid tumor), mesenchymal neoplasms [solitary fibrous tumor (SFT), synovial sarcoma, and dedifferentiated liposarcoma] and various other tumors with spindle cell morphology, that may occasionally involve the anterior mediastinum. The clinical, pathological, immunohistochemical and molecular hallmarks of these lesions will be discussed and useful tips for the differential diagnosis with spindle cell thymoma will be provided.