Gastroesophageal reflux is one of the most common reasons for referrals to paediatricians or paediatric gastroenterologists. Gastric acid-buffering agents, mucosal surface barriers and gastric anti-secretory agents are the main groups of medications currently used for treating gastroesophageal reflux disease (GERD) in children. Recently, the use of proton pump inhibitors (PPIs) for the treatment of GERD in children has increased considerably. Their effectiveness in healing erosive oesophagitis in paediatric subjects and in improving GERD symptoms has been established in many studies. However, the effectiveness in other clinical conditions and the long-term safety of PPIs for paediatric GERD have not been fully established yet and thus are still under debate. Therefore, the aim of this article is to provide a comparative review of the efficacy, safety and tolerability of PPIs in paediatric GERD. The available data suggest that short-term use of PPIs is well tolerated. Adverse events tend to be of a mild-to-moderate nature, with headache being the most frequently reported treatment-related adverse event. However, further well-designed trials and observational studies are still needed to clarify the efficacy and safety of PPIs in the paediatric population, especially in infants under the age of 12 months.