We investigated breakfast eating habits and lifestyle behaviors among Saudi school children attending public versus private schools. A random sample of 1149 children (girls: 54.4%) from public and private schools was selected from elementary schools using the multistage stratified cluster method. Measurements included body weight, height, body mass index (BMI), and self-reported questionnaires filled by the child’s parents. There was no significant (p = 0.44) difference in the prevalence of breakfast intake between children attending public (20.6%) versus private (19.4%) schools. However, there was a gender by school type interactions in breakfast intake frequency, as boys in private but not in public schools had significantly (p = 0.006) higher (26.3%) daily breakfast intake than girls (13.3%). Over 56% of the children ate and drank from the school canteen, and impacting factors on children’s choices were children’s desire, food taste, and parental influence. More parents of children in private (12.1%) than in public (6.9%) schools were satisfied with the food in the school canteen. Younger age (aOR = 0.889, 95% CI = 0.815–0.970, p = 0.008), higher father education (aOR = 1.380, 95% CI = 1.130–1.686, p = 0.002), family income (aOR = 1.227, 95% CI = 1.005–1.498, p = 0.044), and insufficient sleep duration (aOR = 0.740, 95% CI = 0.553–0.990, p = 0.042) were significantly associated with being in a private school. Furthermore, no significant differences, when adjusted for socio-demographic factors, appeared in breakfast intake or overweight/obesity relative to school type. Interventions to improve daily breakfast consumption and lifestyle behaviors of Saudi children are warranted.