Meal-related symptoms are common in paediatric functional dyspepsia (FD). There are only a small number of paediatric studies assessing mechanisms for meal-related symptoms, and these have not utilized Rome IV criteria. The aim of the current study was to assess gastric myoelectric and autonomic nervous system (ANS) responses to both liquid and solid meals in youth with Rome IV-defined FD. In healthy controls (N = 14) and youth with FD (N = 12), we recorded electrocardiograph (to assess heart rate variability; HRV) and electrogastrograph (EGG) signals before and after two test meals, one liquid and one solid. EGG parameters and HRV were assessed for the entire pre- and postprandial periods and in short time intervals. Additionally, liquid gastric emptying was assessed utilizing a 13 C-acetate breath test. During the EGG, the dominant power increased with both meals in controls but not patients with FD. During HRV assessment, the low frequency to high frequency ratio was higher after the liquid meal in controls, despite being similar preprandial, as compared to patients with FD. In controls, both standard deviation of normal to normal waves (SDNN) and root mean square of successive ECG R peaks (R-R interval) differences (rMSSD) increased after the liquid meal (but not after the solid meal) in controls but not patients with FD. Youth with Rome IV-defined FD lacks the normal postprandial EGG dominant power response or autonomic nervous system response following a liquid meal. The latter appears to indicate a lack of ANS flexibility.