This study investigated the relationship between eating behavior and poor glycemic control in 5,479 Japanese adults with hemoglobin A1c (HbA1c) <6.5% who participated in health checks. Respondents to a 2013 baseline survey of eating behavior, including skipping breakfast and how quickly they consumed food were followed up until 2017. We defined poor glycemic control after follow-up as HbA1c ≥6.5%, or increases in HbA1c of ≥0.5% and/or being under medication to control diabetes. We identified 109 (2.0%) respondents who met these criteria for poor glycemic control. After adjusting for sex, age, smoking status, body mass index (BMI), and eating behavior, the risk of poor glycemic control was increased in males (odds ratio [OR], 2.38; 95% confidence interval [CI] 1.37-4.12; p < 0.01), and associated with being older (OR, 1.07; 95% CI, 1.04-1.11; p < 0.001), having a higher BMI (OR, 1.29; 95% CI 1.23-1.35; p < 0.001), skipping breakfast ≥3 times/week (OR, 2.44; 95% CI, 1.35-4.41; p < 0.01), and changing from eating slowly or at medium speed to eating quickly (OR, 2.11; 95% CI, 1.04-4.26; p < 0.05). In conclusion, Japanese adults who were male, older, had a high BMI, skipped breakfast ≥3 times/week and ate quickly were at increased risk for poor glycemic control.