Cystatin could completely cure experimental visceral leishmaniasis by switching the differentiation of Th2 cells to Th1 type, as well as upregulating NO, and activation of NF‐κB played a major role in these processes. Analysis of upstream signaling events revealed that TLR 2/4‐mediated MyD88‐dependent participation of IL‐1R‐activated kinase (IRAK)1, TNF receptor‐associated factor (TRAF)6 and TGFβ‐activated kinase (TAK)1 is essential to induce cystatin‐mediated IκB kinase (IKK)/NF‐κB activation in macrophages. Cystatin plus IFN‐γ activated the IKK complex to induce phosphorylation‐mediated degradation of p105, the physiological partner and inhibitor of the MEK kinase, tumor progression locus 2 (Tpl‐2). Consequently, Tpl‐2 was liberated from p105, thereby stimulating activation of the MEK/ERK MAPK cascade. Cystatin plus IFN‐γ‐induced IKK‐β post‐transcriptionally modified p65/RelA subunit of NF‐κB by dual phosphorylation in infected phagocytic cells. IKK induced the phosphorylation of p65 directly on Ser‐536 residue whereas phosphorylation on Ser 276 residue was by sequential activation of Tpl‐2/MEK/ERK/MSK1. Collectively, the present study indicates that cystatin plus IFN‐γ‐induced MyD88 signaling may bifurcate at the level of IKK, leading to a divergent pathway regulating NF‐κB activation by IκBα phosphorylation and by p65 transactivation through Tpl‐2/MEK/ERK/MSK1.