Introduction: Upper gastrointestinal endoscopies are used for primary and secondary prophylaxis for variceal bleeding in paediatric portal hypertension. Objectives: To analyse the differences of primary and secondary prophylactic endoscopies performed in children with portal hypertension, who receive care at the gastroenterology clinic of Lady Ridgeway Hospital for Children, Sri Lanka. Methods: A retrospective analytical study was carried out among 184 children who received care for portal hypertension, using the clinic records. Data was analysed using SPSS version 25. Results: Initial endoscopy was performed for primary prophylaxis in 78.4% and secondary prophylaxis in 21.6%, respectively . In the secondary group, 19.6% presented with haematemesis and 1.5% with melaena. The common presentations in the primary group were chronic liver cell disease (30.9%), splenomegaly (22.2%), and jaundice (6.2%). Presence of grade 3 varices (p=0.000), red signs (p=0.002), fundal varices (p=0.004) in the initial endoscopy was higher in the secondary group. The number of endoscopy procedures required in the last year (2.14 vs 1.39, p=0.000) was higher in the primary group. The mean number of emergency endoscopies in the last year (0.5 vs 1.3, p=0.002) and mean number of emergency endoscopic therapeutic interventions (0.29 vs 0.73, p=0.021) were higher in the secondary group. Conclusions: The severity of portal hypertension is higher in the initial endoscopies indicated for secondary prophylaxis. The total number of endoscopies required in primary prophylaxis is higher due to frequent repeated elective endoscopies. Requirements for emergency endoscopic procedures and interventions are higher in secondary prophylaxis; performing endoscopies before gastrointestinal bleeding is recommended.