Controversies concerning the association between obesity and acute myocardial infarction (AMI) are still ongoing in Japan. We investigated the association between obesity defined by body mass index of 25 kg/m² or higher and AMI by a case–control study using data from 1199 AMI cases and 4056 apparently healthy controls. The analysis was performed in age- and sex-matched samples of 621 case–control pairs younger than 80 years and in crude samples aged 40–79 years divided into 10-year age groups. Prevalence of obesity, diabetes, current smoking, hypertension, and hypercholesterolemia were compared between cases and controls, and a multivariable odds ratio (OR) of AMI was calculated for each risk factor in various age groups. The OR (95 % confidence interval (CI)) of AMI for obesity was 1.63 (1.23–2.17), P = 0.0008 in men younger than 80 years; 2.65 (1.41–5.00), P = 0.0025 in women younger than 80 years; 2.23 (1.46–3.41), P = 0.0002 in men aged 59 years or younger; 1.34 (0.90–2.01), P = 0.1510 in men aged 60–79 years; and 2.98 (1.56–5.71), P = 0.0010 in women aged 60–79 years using paired samples. The OR (95 % CI) of AMI for obesity was 4.92 (2.53–9.58), P < 0.0001 in men aged 40–49 years; 1.54 (1.07–2.21), P = 0.0197 in men aged 50–59 years; 1.07 (0.69–1.66), P = 0.7717 in men aged 60–69 years; 2.24 (1.20–4.20), P = 0.0118 in men aged 70–79 years; 2.48 (1.12–5.48), P = 0.0245 in women aged 60–69 years; and 3.05 (1.46–6.37), P = 0.0029 in women aged 70–79 years using crude samples. The association between obesity and AMI was age- and gender-dependent in a Japanese population.