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Background: Pneumococcal disease is a leading cause of communicable disease morbidity and mortality globally. We aimed to estimate invasive pneumococcal disease (IPD), pneumococcal pneumonia (PP) and all-cause pneumonia (ACP) incidence rates (IRs) in children aged 0–17 years in England from 2003 to 2019. Methods: A retrospective study in children ≤17 years old from 2003 to 2019 using the Clinical Practice Research Datalink (CPRD) Gold and Hospital Episodes Statistics Admitted Patient Care (HES APC) databases. IPD episodes were identified in hospital records (HES APC). PP (caused by Streptococcus pneumoniae only) and ACP episodes (caused by any pathogen) were identified in primary care (CPRD) and in hospital records (HES APC). Annual IRs by age-group were calculated as the number of episodes/person-years (PY) at risk, with 95% confidence intervals (95% CI). Interrupted time series analyses were conducted to assess changes in IRs across the post-PCV7 (2007–2009), early post-PCV13 (2011–2014) and late post-PCV13 (2015–2019) periods compared to the pre-PCV7 period (2003–2005) using generalized linear models. Results: 170 IPD episodes, 769 PP episodes and 12,142 ACP episodes were identified in 1,500,686 children in 2003–2019. The overall IPD, PP and ACP IRs (per 100,000 PY) were 2.29 (95% CI 1.96–2.66), 10.34 (95% CI 9.62–11.10) and 163.37 (95% CI 160.47–166.30), respectively. The highest IPD, PP and ACP IRs were observed in children aged < 2 years compared to older children (2–4 and 5–17 years). IPD IRs decreased between the pre-PCV7 period and the late post-PCV13 period from 3.28 (95% CI 2.42–4.33) to 1.41 (95% CI 0.80–2.29), IRR 0.28 (95% CI 0.09–0.90), p-value 0.033. PP IRs declined between the pre-PCV7 period and the late post-PCV13 period from 14.65 (95% CI 12.77–16.72) to 3.87 (95% CI 2.81–5.20), IRR 0.19 (95% CI 0.09–0.38), p-value < 0.001. ACP IRs declined between the pre-PCV7 period and the late post-PCV13 period from 167.28 (95% CI 160.78–173.96) to 124.96 (95% CI 118.54–131.63), IRR 0.77 (95% CI 0.66–0.88), p-value < 0.001. Conclusions: The clinical burden of IPD, PP and ACP declined in children in England aged 0–17 years between 2003 and 2019, especially in the late post-PCV13 period. This study highlights the importance of PCV vaccination in reducing the burden of PD and ACP in children in England. [ABSTRACT FROM AUTHOR]