The infection fatality risk indicates the probability of death among infected individuals. The age-dependent heterogeneity of infection fatality risk is crucial for severity assessment and prioritization of countermeasures. However, infection fatality risk estimation requires infection data from a large-scale seroepidemiological survey combined with either direct ascertainment of deaths caused by infection or excess mortality estimates. To overcome the difficulty in ascertaining death, we propose an alternative approach to estimating the age-specific infection fatality risk for SARS-CoV-2 using medicolegal death investigation data in Tokyo with systematic post-mortem polymerase chain reaction testing. We integrated (i) polymerase chain reaction positivity among all deceased individuals at the Tokyo Medical Examiner’s Office, (ii) age-specific all-cause mortality risks from vital statistics, and (iii) age-stratified cumulative infection risks derived from seroepidemiological surveys. Infection fatality risk was computed using Bayes’ theorem. Results showed that infection fatality risk increased steeply with age. Our estimates (0.02% for ages 0–39 years, 0.30%–0.50% for ages 40–64 years, and 3.8%–4.2% for those aged ≥65 years) were consistent with published pre-vaccination meta-analytic estimates. Systematic testing within medicolegal death investigation systems can provide rapid, age-resolved severity assessments, improving the timeliness and comparability of infection fatality risk estimation across jurisdictions.