Small intestinal bacterial overgrowth (SIBO) is a common condition in disorders of gut-brain interaction (DGBI). Recently, a combined scintigraphy-lactulose hydrogen breath test (ScLHBT) was described as an accurate tool diagnosing SIBO. We aim to analyze whether a lactulose nutrient challenge test (NCT), previously shown to separate DGBI from healthy volunteers, is equivalent to ScLHBT in diagnosing SIBO. We studied data of 81 DGBI patients undergoing ScLHBT with 30 g lactulose and 300 mL water as well as NCT with 30 g lactulose and a 400 mL liquid test meal. Differences in proportion of positive SIBO diagnoses according to specified cecal load and time criteria for NCT and ScLHBT, respectively, were tested in an equivalence trial. An odds ratio (OR) range of 0.80-1.25 was considered equivalent. Diagnosis of SIBO during NCT was not equivalent to SIBO diagnosis in ScLHBT, considering a hydrogen increase before cecal load of 5.0%, 7.5%, or 10.0%, respectively ([OR, 3.76; 90% CI, 1.99-7.09], [OR, 1.87; 90% CI, 1.06-3.27], and [OR, 1.11; 90% CI, 0.65- 1.89]). Considering only time to hydrogen increase as criterion, the odds of a positive SIBO diagnosis in the NCT (0.65) was lower than in ScLHBT (1.70) (OR, 0.38; 90% CI, 0.23-0.65). This study could not show an equivalence of NCT and ScLHBT in diagnosing SIBO. A possible explanation might be the different transit times owing to unequal testing substances. The effect of this deviation in relation to consecutive therapy regimens should be tested in further prospective studies.