In England and Wales, replacement of childhood 7-valent pneumococcal conjugate vaccine (PCV7) with a 13-valent vaccine (PCV13) in 2010 was associated with a significant reduction in PCV13-serotype invasive pneumococcal disease (IPD), with a small increase in IPD due to non-vaccine serotypes. Here, we describe the clinical presentation, comorbidity prevalence, serotype distribution and outcomes of childhood IPD during the first 6 years after PCV13 introduction.