Although breakfast programs in schools have been encouraged in school-aged children due to numerous benefits on physical and academic performance, participation in School Breakfast Programs (SBP) remains lower than the National School Lunch Program in the United States. Some studies have found that lower participation in the SBP are due to barriers and stigmas. Some studies have found that when breakfast programs are taken into the classroom, uptake of the program improves. However, the relationship between breakfast intake and academic outcomes among young adolescents remains inconclusive. The goal of this study was to examine the effect of a newly implemented Breakfast in the Classroom (BIC) program within a large urban school district in Western Massachusetts. A secondary comparative cross-sectional analysis was conducted to investigate the impact of the “Breakfast in the Classroom” (BIC) program on middle school students’ academic performance, absenteeism rates, and school nurse visits, factors that influence learners positive experience within the school system. Data on a total of 1,897 students from seven public schools in Western Massachusetts were included in the analysis. Linear regression models showed that breakfast in the classroom (BIC) program did not have a significant effect on student academic performance, attendance, and school nurse visits in a cohort of middle school students. Sensitivity analysis on a subset of the sample of students receiving free lunch who are also participants of the BIC program, had significantly higher academic performance outcomes than their BIC peers who were ineligible for the free lunch program. Findings of the study provide important baseline data for both food services and the school board district and can help inform future studies on the impact of the BIC program on student outcomes.