Hepatic glycogen storage diseases (GSDs) are inborn errors of metabolism whose dietary treatment involves uncooked cornstarch administration and restriction of simple carbohydrate intake. The prevalence of feeding difficulties (FDs) and orofacial myofunctional disorders (OMDs) in these patients is unknown. Objective To ascertain the prevalence of FDs and OMDs in GSD. Methods This was a cross-sectional, prospective study of 36 patients (19 males; median age, 12.0 years; range, 8.0–18.7 years) with confirmed diagnoses of GSD (type Ia = 22; Ib = 8; III = 2; IXa = 3; IXc = 1). All patients were being treated by medical geneticists and dietitians. Evaluation included a questionnaire for evaluation of feeding behavior, the orofacial myofunctional evaluation (AMIOFE), olfactory and taste performance (Sniffin’ Sticks and Taste Strips tests), and facial anthropometry. Results Nine (25%) patients had decreased olfactory perception, and four (11%) had decreased taste perception for all flavours. Eight patients (22.2%) had decreased perception for sour taste. Twenty-six patients (72.2%) had FD, and 18 (50%) had OMD. OMD was significantly associated with FD, tube feeding, selective intake, preference for fluid and semisolid foods, and mealtime stress (p < 0.05). Thirteen patients (36.1%) exhibited mouth or oronasal breathing, which was significantly associated with selective intake (p = 0.011) and not eating together with the rest of the family (p = 0.041). Lower swallowing and chewing scores were associated with FD and with specific issues related to eating behavior (p < 0.05). Conclusion There is a high prevalence of FDs and OMDs in patients with GSD. Eating behavior, decreased taste and smell perception, and orofacial myofunctional issues are associated with GSD.