Probiotics are widely consumed for their potential health benefits, particularly in promoting gastrointestinal health and treating functional gastrointestinal disorders (FGIDs). However, recent studies have raised concerns about the potential association between probiotic use and brain fog, a cognitive dysfunction characterized by confusion, impaired judgment, and lack of focus. A 47-year-old male commercial airline captain with over 10000 flight hours presented with a two-month history of bloating, abdominal distension, and irregular bowel habits following a period of occupational stress and irregular dietary habits. The pilot's previous medical history was largely uneventful, with the exception of a long-standing gastritis diagnosis. To manage this condition, he had been on a daily regimen of 20 mg of pantoprazole for approximately eight years. After a telemedicine consultation, he began taking an over-the-counter probiotic supplement containing 16 strains. Within five days, he experienced a significant exacerbation of abdominal symptoms, accompanied by somnolence, difficulty concentrating, and mental fatigue, raising safety concerns given his profession. Functional gastrointestinal examination revealed a distended abdomen with increased bowel sounds. Probiotic-associated brain fogginess was suspected, and the patient was advised to discontinue the supplements. Rifaximin therapy was initiated, resulting in rapid resolution of both gastrointestinal and cognitive symptoms. The clear temporal association between probiotic intake and symptom onset, followed by resolution after antibiotic treatment, suggests a causal relationship. This case highlights the potential risks of unsupervised probiotic use, particularly in safety-sensitive professions such as commercial aviation. Occupational health physicians and aeromedical examiners should be aware of the potential for probiotic-induced brain fog in airline pilots (APs). Prompt recognition and appropriate antibiotic treatment can result in complete symptom resolution and prevent occupational hazards.