Objective To determine the long-term safety and effectiveness of mesenchymal stem cells (MSCs) for bronchopulmonary dysplasia in premature infants enrolled in our previous phase I clinical trial up to 2 years’ corrected age (CA). Methods In a prospective longitudinal follow-up study up to 2 years’ CA of infants received MSCs (MSC group), we assessed serious adverse events, somatic growth, and respiratory and neurodevelopmental outcomes at visit 1 (4-6 months’ CA), visit 2 (8-12 months’ CA), and visit 3 (18-24 months’ CA), and compared these data with those from a historical case-matched comparison (control group). Results Although 1 out of total 9 infants in the MSC group died of Enterobacter cloacae sepsis at 6 months’ CA, the remaining 8 infants survived without any transplantation-related adverse outcomes, including tumorigenicity. No infant in the MSC group was discharged with home supplemental oxygen, as compared with 22% in the control group. The average re-hospitalization rate in the MSC group was 1.4 due to respiratory infections during 2 years’ of follow up. The mean body weight of the MSC group at visit 3 was significantly higher as compared with that of the control group. No infant in the MSC group was diagnosed with cerebral palsy, blindness, or developmental delay; however, in the control group, 1 infant each was diagnosed with cerebral palsy and developmental delay. Conclusion Intratracheal transplantation of MSCs in preterm infants is safe and effective, with no adverse respiratory, growth, and neurodevelopmental effects at 2 years’ CA.