Germinoma in the basal ganglia (BG) is notorious for its diagnostic difficulty. Clinical and radiological features of this disease are quite diverse, but have not been well characterized with respect to prognosis. We retrospectively reviewed the clinical course and treatment outcomes of 17 patients with a BG germinoma. The initial magnetic resonance imaging (MRI) features were classified. Clinical features and treatment outcomes were then analyzed with this classification scheme. A Type 1 lesion was defined as a subtle lesion with faint or no contrast enhancement (six patients). Type 2, 3, and 4 lesions were defined as contrast-enhancing lesions and were differentiated by the lesion size and the presence of subependymal seeding (11 patients). Type 1 lesions were distinct from the other lesions. Patients with a Type 1 lesion had a significantly longer time from the initial MRI to diagnosis than patients with Type 2, 3, and 4 lesions (P = 0.012). The actuarial progression-free survival and overall survival of patients 5 years after diagnosis were 66 and 77%, respectively. The presence of a Type 1 lesion (P = 0.004), a longer time delay in the diagnosis (P = 0.038), and radiation therapy without complete ventricular coverage (P = 0.010) were significantly associated with tumor progression. Profound motor deficits at diagnosis were associated with deterioration in motor function after tumor remission (P = 0.035). Early diagnosis of BG germinomas could affect the ability to control a tumor and neurological outcomes. In particular, high clinical suspicion and active diagnostic procedures are recommended. For optimal treatment, radiation fields should include entire ventricles even if there is no subependymal seeding.