Pneumococcal Ser/Thr kinase (StkP) and its cognate phosphatase (PhpP) play a crucial role in bacterial cytokinesis. Unlike homologs of PhpP in other gram-positive pathogens, the precise role of PhpP in pneumococcal virulence is presently unknown since most available studies on these proteins are carried out using unencapsulated pneumococcal strains. Here, we demonstrate that the encapsulated pneumococcal strain D39-derived ΔPhpP and ΔStkP mutants grow differentially in the presence of different non-glucose carbohydrate sources. Microscopic analysis and RNA-seq-based Global transcriptome analysis including virulence genes-specific transcript abundance displayed significantly down- and up-regulation of the capsule in D39ΔPhpP and D39ΔStkP mutants respectively. This reciprocal regulation was not observed with several other genes indicating that kinase and phosphatase activity of StkP and PhpP act both cognately with as well as independent of each other. Along with these results, the attenuation of virulence in the ΔPhpP mutant as compared to the wild-type strain corroborated with several downregulated virulence-related genes. Despite the upregulation of capsule related genes and increased capsule production, the mutants lacking StkP displayed significantly decreased virulence or delayed onset of infection in mice. The wild-type phpP- as well as stkP-gene complemented respective mutant strains displayed restoration of these lost functions. Our results thus revealed that both PhpP as well as StkP play a crucial role in the modulation of pneumococcal metabolic fitness and virulence. PhpP couls serve as an important therapeutic target for the development of a novel attenuated vaccine or a small molecule-based antivirulence agent.