Central nervous system infections can have devastating clinical outcomes if not diagnosed and treated promptly. There is a documented gap between recommended and actual practice and a limited understanding of its causes. We identified and explored the reasons for this gap, focusing on points in the patient pathway most amenable to change and the development of a tailored intervention strategy to improve diagnosis and treatment. Using theoretically-informed semi-structured interviews, we explored barriers and enablers to diagnosing and managing patients with suspected encephalitis, specifically performing lumbar punctures and initiating antiviral therapy within 6 h. We purposively sampled hospitals and hospital staff in the UK. We audio recorded and transcribed all interviews prior to a framework analysis. We mapped identified barriers and enablers to the patient pathway. We matched behaviour change techniques targeting clinicians to the most salient barriers and enablers and embedded them within an intervention package. We interviewed 43 staff in six hospitals. Clinical staff expressed uncertainty when and how to perform lumbar punctures and highlighted practical difficulties in undertaking them within busy clinical settings. Once treatment need was triggered, clinicians generally felt able to take appropriate therapeutic action, albeit within organisational and resource constraints. Matched behaviour change techniques largely targeted antecedents of treatment. These included decision support to prompt recognition, highlighting the consequences of missed diagnoses for clinicians and patients, and practical support for lumbar punctures. We subsequently devised an evidence-informed package comprising 'core' interventions and, to allow for local flexibility, 'optional' interventions. We identified several points in the patient pathway where practice could improve, the most critical being around clinical suspicion and initial investigation. Interventions targeting professional beliefs and behaviours whilst optimising their clinical environment were amongst the most promising approaches to improve the care of suspected encephalitis. Randomised trial registered with Controlled Trials ISRCTN06886935 .