Introduction: Children with chronic conditions exhibit an increased rate of severe acute illnesses requiring pediatric critical care. Some of these children receive mechanical ventilation; however, the subcategory of chronic conditions requiring mechanical ventilation and associated with mortality risk in children remains unclear. Hypothesis: The objective of this study was to delineate the risk of PICU mortality and prolonged duration of mechanical ventilation and PICU stay in children with chronic conditions requiring mechanical ventilation in the PICU. Methods: A retrospective cohort study was conducted in a 10-bed PICU in a tertiary children’s hospital in Japan. We reviewed all intubation cases in the PICU between April 2008 and July 2012. We recorded age, sex, Pediatric Index of Mortality 2 (PIM2) scores, main reason for admission, history of chronic conditions, duration of mechanical ventilation, duration of PICU stay, and mortality throughout the study period. Results: During the study period, 351 children underwent mechanical ventilation, of which 10.0% exhibited more than two chronic conditions, 40.4 % exhibited one chronic condition, and 49.6 % exhibited no chronic condition. Children with chronic conditions were not associated with mortality or prolonged duration of PICU stay. Of the various chronic subcategories, the subcategory of hematological/oncological chronic conditions was associated with significantly greater odds of PICU mortality [odds ratios, 4.77; 1.18–12.5); p < 0.01] and significantly longer duration of mechanical ventilation (p = 0.021) compared with non-hematological/oncological chronic conditions. There was no difference in PIM2 scores between the two groups (p = 0.251). Respiratory, cardiac, central nervous, gastrointestinal, and other chronic conditions were not associated with increased odds of PICU mortality and duration of mechanical ventilation. Conclusions: Children with one or more than two chronic conditions are not at a greater risk for PICU mortality and prolonged duration of PICU stay compared with children with no chronic condition. PIM2 scores were not increased in either group; however, hematological/oncological chronic conditions were associated with an adverse outcome.