Background: Breakfast has traditionally been considered one of the most important meals of the day; however, there is little evidence for the influence of breakfast quality and insulin resistance (IR). This study aimed to assess the quality of breakfast in a group of schoolchildren, and its association with IR. Methods: A cross-sectional study with 852 children (8–13 years) was carried out. Fasting plasma glucose, insulin and anthropometric parameters were measured. A three-day dietary record was used to assess their diet and to calculate the Breakfast Quality Index (BQI). The sample was divided into tertiles according to the BQI (tertile 3: better breakfast quality). The homeostatic model was used to assess insulin resistance (HOMA-IR), and IR was defined as HOMA-IR > 3.16. Results: The prevalence of IR was 5.2%. The mean BQI score was 4.50 ± 1.25, and boys had lower scores than girls. Children in the BQI tertile 3 had a better global diet quality. In boys, being in the BQI tertile 3 was associated with a lower risk of IR (OR [95% CI]: 0.10 [0.01–0.77], p < 0.05). Conclusions: A higher-quality breakfast was associated with better overall diet quality and a lower risk of IR, especially in boys.