Background Comprehensive geriatric assessment (CGA) is a multidimensional and multidisciplinary method to identify geriatric conditions among older patients. The aim of the present study was to examine the associations between CGA and short-term outcomes among older adult inpatients with stroke. Methods The study was a nationwide, retrospective cohort study. We used the Diagnosis Procedure Combination database, a national Japanese inpatient database, to identify older adult stroke patients from 2014 to 2017. The associations between CGA and in-hospital mortality, length of hospital stay, readmission rate, rehabilitation intervention, and introduction of home health care were evaluated using propensity score matching and instrumental variable analysis. Findings We identified 338,720 patients, 21·3% of whom received CGA. A propensity score-matched analysis of 53,861 pairs showed that in-hospital mortality was significantly lower in the CGA group than in the non-CGA group (3·6% vs. 4·1%, p 60 days) was significantly lower in the CGA group than in the non-CGA group (8·7% vs. 10·1%, p < 0·001), and the rates of rehabilitation intervention (30·3% vs. 24·9%, p < 0·001) and home health care (8·3% vs. 7·6%, p = 0·001) were both higher in the CGA group than in the non-CGA group. Instrumental variable analysis showed similar results. Interpretation CGA was significantly associated with the examined short-term outcomes. These findings from Japan, one of the most aged countries worldwide, highlight the possible benefits of CGA for short-term outcomes and can be of use for health policy in other international contexts. Funding This work was supported by grants from the Ministry of Health, Labour and Welfare, Japan (19AA2007 and H30-Policy-Designated-004) and the Ministry of Education, Culture, Sports, Science and Technology, Japan (17H04141).