The exposure of a positively charged residue, lysine11 (Lys11), at the N-terminus following proteolytic cleavage of the Lys10-Lys11 peptide bond, is necessary for the plasminogen activation by staphylokinase (SAK) from Staphylococcus aureus. However, in many natural variants of SAK, Lys11 is substituted by isoleucine (Ile) or valine (Val). The role of these N-terminal amino acid substitutions in modulating the plasminogen activation ability of SAK remains unknown. To investigate the molecular mechanism by which Lys11 and its substitutions at the N-terminus of SAK modulate its plasminogen activation potentiality, we performed substitution and deletion mutagenesis of Lys11, combined with structural modelling of bimolecular complexes of these mutants with micro-plasmin. SAK mutants carrying substitutions of Lys11 with Ile or Val exhibited N-terminal processing and catalytic efficiency for plasminogen activation comparable to wild-type SAK. In contrast, the substitution of Lys11 with alanine (Ala) drastically reduced its plasminogen activation ability, despite maintaining N-terminal processing similar to wild-type SAK. These findings suggest that Lys11 at the N-terminus of SAK can be functionally replaced with Ile or Val. However, unlike streptokinase, the presence of Ile at the N-terminus of SAK does not enable non-proteolytic activation of plasminogen. Structural models of SAK and its mutants in complex with micro-plasmin revealed that the flexible N-terminus extends towards the active site at the interphase of Asp646 within a distance of 4 Å, favouring direct interactions between the exposed Lys, Ile, or Val residues similar to other serine proteases, thereby altering substrate specificity of plasmin towards plasminogen activation.