Limited information is available on clinicians’ advising practices and perceived familiarity of probiotics in the management of childhood functional abdominal pain disorders (FAPDs) and functional defecation disorders (FDD). This study aimed to investigate pediatricians’ and general practitioners’ (GPs) advising practices and perceived familiarity of probiotics in the management of FAPDs and FDD. A cross-sectional survey was administered to Dutch pediatricians and GPs, including 27 questions about perceived familiarity of probiotics, followed by questions related to advising practices and reasons for advising or not advising probiotics. The responses of 319 pediatricians and 67 GPs were included. Significantly more pediatricians indicated to be familiar with probiotics compared to GPs (71% vs. 48% respectively, p < 0.001). Significantly more pediatricians advised probiotics compared to GPs for FAPDs (54% vs. 25%, respectively, p < 0.001) and for FDD (17% vs. 7%, respectively, p < 0.05). Primary reason to advise probiotics was patient request; main reason not to advise probiotics was personal lack of knowledge regarding probiotic use. Conclusions: Increased familiarity and appropriate advising of probiotics in treatment of childhood FAPDs and FDD among pediatricians and GPs is required. Improved familiarity of probiotics is important to provide appropriate information about probiotic use to children and caregivers and may facilitate shared decision-making.