Many African counties, like Kenya, have introduced pneumococcal conjugate vaccines (PCVs) with financial support from Gavi, the Vaccine Alliance. However, in the near future, they are expected to transition and take up the full costs. Kenya introduced the ten-valent PCV (PCV10) in 2011 and enters the accelerated transition phase in 2022. This work aimed to study the effects of PCV10 vaccination on pneumococcal carriage and disease in the pre- and the immediate post-vaccination period, predict the long-term vaccination impact on carriage of pneumococcus and subsequent invasive pneumococcal disease, evaluate immune factors that may influence that impact and, ultimately, investigate the cost-effectiveness of potential policy options in order to guide Kenya’s decision-making. A dynamic transmission model was fitted to pre-vaccination carriage data and its predictions were validated against post-vaccination carriage data. In order to evaluate immune factors that may influence vaccination impact and thus warrant consideration in the mathematical model, statistical modelling of the association between pre-existing pneumococcal carriage and vaccine responsiveness, and between maternally-derived anti-protein and anti-capsular antibodies and the rate pneumococcal acquisition in newborns, was undertaken. A cost-effectiveness analysis was done based on the disease incidence predictions from the transmission model. The dynamic transmission model was shown be useful as it closely predicted the observed magnitude and timing of serotype replacement. Maternal anti-capsular antibodies were estimated to have a limited role while impaired immune responses were observed among vaccine serotype carriers at the point of vaccination. These two immune factors were evaluated within the decision making structure and considered to have negligible impact on the performance of the model. In the conclusion, I estimated that sustaining PCV10 vaccination in Kenya will be cost-effective but will present a significant challenge to affordability by the Kenyan Government.