Background: Pneumonia is the leading infectious cause of childhood mortality worldwide, and more than half of child pneumonia-related deaths occur in sub-Saharan Africa. Streptococcus pneumoniae is the most common bacterial cause of childhood pneumonia. Few data exist regarding the effect of 13-valent pneumococcal conjugate vaccine (PCV-13) on pneumonia risk among African children. PCV-13 was introduced into Botswana's Expanded Programme of Immunizations (EPI) in July 2012. Methods: We conducted a retrospective review of hospital admission registers from the two largest referral hospitals and one large district hospital in Botswana. We recorded children 1 to 59 months of age who were hospitalized with a discharge diagnosis of pneumonia from January 2008 to December 2017. We compared the number of pneumonia-related hospitalizations during the pre-vaccine period (2008-2012) to early post-vaccine (2013-2015) and late post-vaccine (2016-2017) periods using Poisson regression. To evaluate for changes in hospital referral patterns, we compared the number of hospitalizations for ingestion (a diagnosis unrelated to vaccination) during these same periods. Results: There were 7785 pneumonia hospitalizations and 1589 ingestion hospitalizations during the study period. The annual number of pneumonia hospitalizations was 1268, 832, and 750 in the pre-vaccine, early post-vaccine, and late post-vaccine periods, respectively. Compared to the pre-vaccine period, pneumonia hospitalizations declined 34% (incidence rate ratio [IRR]: 0.66, 95% confidence interval [CI]: 0.62, 0.70) in the early post-vaccine period and 41% (IRR: 0.59, 95% CI: 0.55, 0.64) in the late post-vaccine period. By comparison, ingestion hospitalizations increased 31% and 15% from the pre-vaccine to early post-vaccine and late post-vaccine periods, respectively. Conclusions: There was a significant decrease in the incidence of pneumonia-related hospitalizations among children in Botswana following the introduction of PCV-13 to the national immunization program. This effect persisted five years after vaccine introduction, supporting long-term efficacy of the vaccine against childhood pneumonia in sub-Saharan Africa.