A low fermentable oligosaccharide, disaccharide, monosaccharide, and polyol (FODMAP) diet has been recommended for irritable bowel syndrome (IBS) patients. This study compared the efficacy of two types of dietary advice: (1) brief advice on a commonly recommended diet (BRD), and (2) structural individual low-FODMAP dietary advice (SILFD). Patients with moderate-to-severe IBS were randomized to BRD or SILFD groups. Gastrointestinal symptoms, 7-day food diaries, and post-prandial breath samples were evaluated. The SILFD included (1) identifying high-FODMAP items from the diary, (2) replacing high-FODMAP items with low-FODMAP ones by choosing from the provided menu. The BRD included reducing traditionally recognized foods that cause bloating/abdominal pain and avoidance of large meals. Responders were defined as those experiencing a ≥30% decrease in the average of daily worst abdominal pain/discomfort after 4 weeks. Sixty-two patients (47 F, age 51 ± 14 years), BRD (n = 32) or SILFD (n = 30), completed the studies. Eighteen (60%) patients in SILFD vs. 9 (28%) in the BRD group fulfilled responder criteria (p = 0.001). Global IBS symptom severity significantly improved and the number of high-FODMAP items consumed was significantly decreased after SILFD compared to BRD. Post-prandial hydrogen (H2) breath production after SILFD was significantly lower than was seen after BRD (p < 0.001). SILFD was more effective than BRD. This advice method significantly reduced FODMAP intake, improved IBS symptoms, and lowered intestinal H2 production.