Encephalitis is widely recognized as a challenging condition to diagnose and manage. The care of patients with encephalitis typically involves multiple disciplines, including neurologists and infectious disease (ID) physicians. Our objective was to describe the perspectives and needs of ID physicians regarding encephalitis, using a cross-sectional questionnaire survey. We performed a survey among physician members of the Infectious Diseases Society of America's (IDSA) Emerging Infections Network (EIN). Response rate was 33% (480 among 1472 active EIN physician members). More than 75% of respondents reported caring for patients with suspected encephalitis. Although one-third were involved in the care of multiple patients with autoimmune encephalitis (AE) annually, comfort in diagnosing and managing encephalitis, and in particular AE, was low. Experience with advanced diagnostic tools was variable, as were approaches toward deployment of such tools. Respondents noted that training could be improved by incorporating a multidisciplinary approach taking advantage of online and virtual platforms. ID physicians report a heavy reliance on the 2008 IDSA guidelines for the management of encephalitis, and indicated strong support for a formal update. ID physicians play an important role in the diagnosis and management of all-cause encephalitis. Despite exposure to AE, few ID physicians are comfortable in recognizing, diagnosing, and treating AE. Moreover, comfort with and use of advanced diagnostic tools for infectious encephalitis was highly variable. Training in encephalitis should include a focus on use and stewardship of advanced diagnostic tools and on collaborative approaches with neurologists and other practitioners on mechanisms and clinical presentations of AE. There is a need for a formal update of 2008 guidelines on the management of encephalitis.