Imaging a case of autoimmune encephalitis (AIE) can be challenging as the underlying tumor may be occult. The aim of this retrospective case-based study is to evaluate role of whole-body MRI/Positron emission tomography (PET) in workup of AIE. Standardizing the whole-body MRI/PET protocol, Cross modality yield with serology and magnetic resonance/PET (MR/PET) and finally highlight the advantage of hybrid MR/PET. We present the retrospective review data from January 2016 to December 2019 referred for whole body MR/PET with suspected AIE/Paraneoplastic syndrome, per consensus criteria, treated at a single tertiary center. Analysis is done group wise based on referral being for oncological, immunological or neuropsychiatric condition. Detailed results with sensitivity and specificity are presented in tabular format with case-based review in our series for protocols and advantages of MR/PET. Among total of 600 MR/PET cases, 227 were suspected of AIE/paraneoplastic syndrome and were referred for whole body imaging. Distribution of Group 1 Known oncology group (n = 10), Group 2 Non oncological systemic illness group (n = 174) and group 3 the primary neuropsychiatric illness (n = 43) with Group 2 being largest. The gender distribution was similar and mean age was 42 years. Seronegative cases (n = 130) were greater than seropositive cases (n = 97). Seropositivity was in the following order Autoimmune > Paraneoplastic > Myositis panel. Whole body MRPET yielded occult malignancy in 9% and imaging abnormality in 88% of cases. Whole body MR/PET has an important role in workup of AIE. Selection of the appropriate protocol is important, especially when history and physical examination are nonspecific.