Procedural sedation for bone marrow examination (BME) and intrathecal chemotherapy (ITC) is necessary for pediatric patients with hematological malignancies. There has been no report on adverse events after discharge from the recovery room. This retrospective study evaluated the types and incidences of delayed adverse events among pediatric patients scheduled for BME or ITC under deep sedation in a single center for 3 years. The patients were divided into two groups: inpatients (group I) and outpatients (group O). All patients were managed during the procedures and the recovery period. In total, 10 adverse events were assessed; these occurred 2 h (T1, acute), 12 h (T2, early), and 24 h (T3, delayed) after the procedure. The duration of each adverse event was also recorded and was classified as 2 h (D1), 12 h (D2), or 24 h (D3). The data of 263 patients (147 inpatients and 116 outpatients) who met the inclusion criteria were analyzed. The overall incidence of adverse events was statistically significant difference: 48.3% in group I and 33.6% in group O ( = 0.011). The rates of adverse events at T1 and T2 were significantly different between groups I and O (42.8% vs. 11.2% and 7.5% vs. 20.7%, respectively) ( < 0.001). The adverse events were mostly of D1 or D2 duration in both groups. Patients with a higher proportion of ketamine in a propofol-ketamine mixture had a significantly higher proportion of adverse events at T1 (34.6%), as compared with those with a mixture with a lower proportion of ketamine (21.1%) or propofol alone (17.9%) ( = 0.012). The most common adverse events were dizziness or headache; typically, they did not last longer than 12 h. The propofol-ketamine combination with a higher proportion of ketamine seems to produce more adverse events within 2 h after the procedure. Nevertheless, all sedative types appear safe to use without additional management.