Background Surveillance for adverse events following immunization (AEFI) is important to monitor vaccine safety and should lead to appropriate responses to improve health and immunization program. Bleeding following vaccination is not recognized as an important AEFI. Without policy of vitamin K (VK) prophylaxis at birth, vitamin K deficiency bleeding (VKDB) could be an important cause of bleeding in young infants and may manifest as AEFI. Methods We retrospectively analysed all serious AEFI cases that presented with external or internal bleeding reported to Nepal’s AEFI surveillance system during 2016–2018. The cases were classified as VKDB, suspected VKDB or non-VKDB. Results During the period, 16 serious AEFI with symptom or sign of bleeding were reported representing 21.3% of all serious AEFI reported. Cases were between 40 and 94 days of age. The National AEFI Investigation Committee classified all cases as coincidental. Fourteen cases (87.5%) had bleeding from injection site. Median time from vaccination to injection site bleeding was 4.3 h (interquartile range: 2.1–11.6 h). Six cases (37.5%) had intra-cranial haemorrhage. Only one case had confirmed history of receiving VK at birth. Ten cases (62.5%) received appropriate treatment (VK injection; blood transfusion if needed). Based on limited laboratory investigations available, three cases (18.75%) could be classified as late onset VKDB and 11 cases (68.75%) as suspected late onset VKDB. Conclusion VKDB should be suspected in young infants presenting with bleeding including following vaccination, and prompt treatment should be initiated. Bleeding following vaccination should be recognized as an important AEFI as even a small amount of blood loss in young infants can be catastrophic. We posit that this series is a small subset of VKDB cases in Nepal detected through AEFI surveillance system. In countries without policy of VK prophylaxis at birth including Nepal, the policy should be introduced.