The important role of Ser/Thr kinase and phosphatase in Streptococcus pyogenes (group A Streptococcus, GAS) physiology and pathogenesis is now well-established. Since GAS genomes do not contain an obvious gene encoding a typical bacterial-type tyrosine kinase (BY-kinase) but contain an orphan gene encoding protein Tyr-phosphatase (SP-PTP), it is presumed that Tyr-phosphorylation does not exist in GAS. Hence, its importance in GAS pathogenesis has remained completely unexplored. Our previous report demonstrating the ability of SP-PTP to dephosphorylate Abl-tyrosine kinase-phosphorylated MBP and identification of phosphorylated Tyr101-residue in the autophosphorylated SP-STK prompted us to hypothesize that a novel putative tyrosine kinase and Tyr-phosphorylation exist in GAS. To identify a genuine Tyr-protein kinase, we performed a genome-wide search of kinases possessing a classical Walker motif. To that end, we first identified and purified a genuine but a non-canonical tyrosine kinase M5005_Spy_1476, a ~17 kDa protein (153 aa) (SP-TyK), which autophosphorylated in the presence of ATP. Both in vitro and in vivo phosphoproteomic analyses revealed two key phosphorylated tyrosine residues located within the catalytic domain of SP-TyK. An isogenic ΔSP-TyK mutant derived from the M1T1 strain grew poorly in THY-medium, and displayed defective cell division and long chains with multiple parallel septa, often resulting in aggregates. Additionally, the mutant displayed an altered Tyr-phosphorylated protein profile and attenuation of virulence in the mouse infection model. The sp-tyk-complemented strain restored the lost functions. Together, these results indicated that SP-TyK-mediated post-translational modifications at Tyr-residues of certain targets directly play a critical role in GAS pathophysiology, morphogenesis, and pathogenesis.