Ribosomal protein S6 kinase (S6K1), a major downstream effector molecule of mTORC1, regulates cell growth and proliferation via modulating protein translation and ribosomal biogenesis. We have previously identified eIF4E as an intermediate in transducing signals from mTORC1 to S6K1 and further demonstrated that the role of mTORC1 is restricted to relieving S6K1 auto-inhibition to allow hydrophobic motif (HM) phosphorylation of the enzyme for activation. These observations rule out the role of mTORC1 as an HM kinase of S6K1 and point towards the involvement of mTORC1 independent kinase in mediating HM phosphorylation. Here, we report mTORC2 as an in-vivo HM kinase of S6K1. We show that S6K1 truncation mutant, incapacitated to respond to mTORC1 signals, continues to display HM phosphorylation which remains sensitive towards mTOR kinase inhibitor-torin 1. Furthermore, we identify a highly conserved amino acid stretch in S6K1 responsible for mediating HM phosphorylation. We show that deletion of this stretch leads to HM dephosphorylation and subsequent in activation of the enzyme. We, therefore, propose a novel mechanism for S6K1 regulation where mTOR complex 1 and 2 act in tandem to activate the enzyme.