Short bowel syndrome (SBS) is a cause of significant morbidity and mortality in children. Probiotics, due to their beneficial effects on the gastrointestinal tract (e.g., improving gut barrier function, motility, facilitation of intestinal adaptation and decreasing pathogen load and inflammation) may have a therapeutic role in the management of SBS. To conduct a systematic review of the current evidence for the effects of probiotic supplementation in children with SBS, the standard Cochrane methodology for systematic reviews was used. The databases, Pubmed, Embase, ACTR, CENTRAL, and the international trial registry, and reference lists of articles were searched for randomised (RCT) or quasi-randomised controlled trials reporting on the use of probiotics in SBS. Our search revealed no RCTs on the use of probiotics in children with SBS. We found one small cross-over RCT (placebo controlled crossover clinical trial), one case control study and nine case reports on the use of probiotics in children with SBS. In the crossover RCT, there was no consistent effect on intestinal permeability (primary outcome) after supplementation with Lactobacillus rhamnosus (LGG) in nine children with SBS. The case control study (four cases: four controls) reported a trend for increase in height and weight velocity and improvement in non-clinical outcomes, such as gut flora, lymphocyte count and serum prealbumin. Five of the nine case reports showed that children (n = 12) with SBS were benefited (e.g., cessation of diarrhoea, improved faecal flora, weight gain and weaning from parenteral nutrition) by probiotic supplementation. The remaining four reported on the adverse effects, such as Lactobacillus sepsis (n = 3) and d-lactic acidosis (n = 2). There is insufficient evidence on the effects of probiotics in children with SBS. The safety and efficacy of probiotic supplementation in this high-risk cohort needs to be evaluated in large definitive trials.