Background: Atypical parkinsonism (AP) often presents with Parkinson’s symptoms but has a much worse long-term prognosis. The diagnosis is presently based on clinical criteria, but a cerebral positron emission tomography (PET) scan with [¹⁸F]fluoro-2-deoxy-2-d-glucose ([¹⁸F]FDG) may assist in the diagnosis of AP such as multiple system atrophy (MSA), progressive supranuclear palsy (PSP), corticobasal degeneration (CBD), and Lewy body dementia (DLB). Only few studies have evaluated the sensitivity and specificity of [¹⁸F]FDG PET for separating the diseases in a mixed patient population, which we aim to assess in a retrospective material. Results: We identified 156 patients referred for a cerebral [¹⁸F]FDG PET for suspicion of AP during 2017–2019. The [¹⁸F]FDG PET was analysed by a nuclear medicine specialist blinded to clinical information but with access to dopamine transporter imaging. The reference standard was the follow-up clinical diagnosis (follow-up: 6–72 months). The overall accuracy for correct classification was 74%. Classification sensitivity (95% confidence interval, CI) and specificity (95% CI) for MSA (n = 20) were 1.00 (0.83–1.00) and 0.91 (0.85–0.95), for DLB/Parkinson with dementia (PDD) (n = 26) were 0.81 (0.61–0.93) and 0.97 (0.92–0.99) and for CBD/PSP (n = 68) were 0.62 (0.49–0.73) and 0.97 (0.90–0.99). Conclusions: Our results support the additional use of [¹⁸F]FDG PET for the clinical diagnosis of AP with moderate to high sensitivity and specificity. Use of [¹⁸F]FDG PET may be beneficial for prognosis and supportive treatment of the patients and useful for future clinical treatment trials.