Background: It is reported that the decline in breakfast consumption is associated with diabetes, metabolic disease, and cardiovascular disease. This study analyzed the association between skipping breakfast and the homeostasis model assessment of insulin resistance (HOMA-IR) and atherosclerotic cardiovascular disease (ASCVD) risk among non-diabetic Korean adults aged 40–79 years who did not take medication for hypertension or dyslipidemia. Methods: This study included 1,001 adults from the Sixth Korea National Health and Nutrition Examination Survey in 2015. Participants were classified into two groups based on those who skipped breakfast and those who ate breakfast. Analysis of covariance was performed to compare the average value of HOMA-IR between the two groups. Logistic regression analysis was used to evaluate the relationship between skipping breakfast and HOMA-IR and ASCVD risk. All analyses were performed after adjusting for covariates. Results: There was no significant association between the group that skipped breakfast and HOMA-IR or ASCVD risk. However, the odds ratio of ASCVD risk was 3-fold higher in male in the skipping breakfast group that skipped breakfast than in those that ate breakfast. Conclusion Previous studies that suggested there was an association between skipping breakfast and ASCVD risk may have been biased as they included individuals taking medication, and thus, this could have led to incorrect results. Therefore, further studies on the association between breakfast consumption and ASCVD risk should consider practical factors that can affect eating habits, such as regular medication use in their analysis.