Background: Medical certification of cause of death (MCCD) is the formal document in which the doctor records the time, causes and circumstances of death of an individual. Inaccuracies and incomplete MCCD will lead to biased estimation of several epidemiological parameters. Hence this study was done to determine the knowledge and practice of MCCD among junior doctors and assess the association between knowledge and some selected variables of interest.Methods: A cross-sectional study was conducted among junior doctors constituting of interns, junior residents and post-graduates trainees of a tertiary hospital of Manipur from February to March 2020. A semi-structured, self-administered questionnaire was used. Data was entered in MS Excel and exported to SPSS version 21 where analysis was done. Descriptive statistics and Chi-square test was used for analysis and p<0.05 was taken as significant. Ethical clearance was obtained from the Institutional ethics committee.Results: Out of the 334 total respondents females constituted 53%. Only 88(26.3%) had satisfactory knowledge, and only 14% (47) of the respondents had ever issued MCCD.No significant association was seen between knowledge score and current department of posting, current designation, gender, religion and work experience.Conclusions: Only a quarter of the respondents (26.3%) were having satisfactory knowledge. There is a need to organize frequent workshops, seminars and induction training highlighting the importance of MCCD for the junior doctors with regular audits.