Non-tuberculous mycobacteria (NTM) illness is an emerging life-threatening infection, and paediatric features have not been well studied. The objective of our study was to review the NTM isolates of hospitalized paediatric patients identified at our institution and to describe the characteristics of these cases. Our retrospective chart review from 2010 to 2013 identified 45 patients with 46 positive NTM cultures. Fifteen (33%) patients had received haematopoietic cell transplant, 13 (29%) had cystic fibrosis, and six (13%) were previously healthy. Twenty-seven (59%) NTM isolates were Mycobacterium chelonae/abscessus, 14 (30%) were M. avium intracellulare, and four (9%) were M. immunogenum. The majority (65%) of cases were community-acquired, and 20 (43%) patients were treated as infection. This case series identified a predominance of M. chelonae/abscessus, and includes a substantial number of haematopoietic cell transplant patients, which reflects the changing spectrum of NTM disease as molecular diagnostics improve and quaternary care facilities provide for a larger immunocompromised population.