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Introduction: A diet low in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAP) has been shown to reduce symptoms among adult patients and children with irritable bowel syndrome. There are no studies investigating the effectiveness of the low FODMAP diet in pediatric patients with functional abdominal pain (FAP). Objective: The study aimed to evaluate the effectiveness of the low FODMAP diet in reducing gastrointestinal symptoms in children with FAP in comparison to the control diet based on the National Institute for Health and Care Excellence (NICE) guidelines. Methods: Twenty-seven children with diagnosed FAP were randomized to 2 groups. Each group received an intervention: the low FODMAP diet or the diet based on NICE. All food was prepared and delivered by a catering company. Data regarding gastrointestinal symptoms were recorded by participants during the 2-week baseline assessment and 4-week dietary intervention. The frequencies of abdominal pain and stools were reported as a number of events per day. The severity of abdominal pain was assessed using the Wong-Baker FACES Pain Rating Scale. The assessment of stool consistency was based on the Bristol Stool Form Scale. Results: The tendency toward the improvement in abdominal symptoms was noted in the low FODMAP group but without statistical significance. No significant differences in stool consistency were observed in this group. The NICE group experienced significant reduction in abdominal pain intensity and frequency (p < 0.01) and improvement in stool consistency (93% reporting normal stool, p < 0.05). Conclusions: The results of this pilot study suggest that the low FODMAP diet is not effective in the reduction of symptoms in children with FAP.