This randomized, double-blind, parallel and placebo-controlled study aimed to evaluate the effect of Bacillus coagulans GBI-30, 6086® probiotic (GanedenBC®) against upper respiratory tract infections (URTI) and gastrointestinal tract infections (GITI) in eighty healthy school-aged children (6-8 years old). The participants received daily a sachet containing either GanedenBC (1 × 10 colony-forming units) or placebo (maltodextrin) for three months. GanedenBC significantly decreased the incidence of URTI symptoms including nasal congestion, bloody nasal mucus, itchy nose, and hoarseness. The duration of the URTI-associated symptoms of hoarseness, headache, red eyes, and fatigue was also decreased. GanedenBC supplementation also significantly reduced the incidence rate of flatulence. These beneficial effects were associated with the modulation of serum TNFα, CD163, G-CSF, ICAM-1, IL-6, IL-8, MCP-2, RAGE, uPAR, and PF4. Therefore, probiotic B. coagulans GBI-30, 6086 modulated immune-related proteins in healthy children, decreasing several URTI and GITI symptoms, thus, this functional ingredient may contribute to a healthier lifestyle.