Suspected central nervous system (CNS) infections may pose a diagnostic challenge, and often concern severely ill patients. We aim to identify predictors of unfavourable outcome to prioritize diagnostics and treatment improvements. Unfavourable outcome was assessed on the Glasgow Outcome Scale at hospital discharge, defined by a score of 1 to 4. Of the 1152 episodes with suspected CNS infection, from two Dutch prospective cohorts, the median age was 54 (IQR 37–67), and 563 episodes (49%) occurred in women. The final diagnoses were categorized as CNS infection (N = 358 episodes, 31%), CNS inflammatory disease (N = 113, 10%), non-infectious non-inflammatory neurological disorder (N = 388, 34%), non-neurological infection (N = 252, 22%), and other systemic disorder (N = 41, 4%). Unfavourable outcome occurred in 412 of 1152 (36%), and 99 died (9%). Predictors for unfavourable outcomes included advanced age, absence of headache, tachycardia, altered mental state, focal cerebral deficits, cranial nerve palsies, low thrombocytes, high CSF protein, and the final diagnosis of CNS inflammatory disease (odds ratio 4.5 [95% confidence interval 1.5–12.6]). Episodes suspected of having a CNS infection face high risk of experiencing unfavourable outcome, stressing the urgent need for rapid and accurate diagnostics. Amongst the suspected CNS infection group, those diagnosed with CNS inflammatory disease have the highest risk.