We derive the generalized Skyrme model as a low-energy effective model of the Sakai-Sugimoto model. The novelty with the past is the presence of the sextic term equal to the topological charge squared. This term appears when the $omega$ meson, and the tower of states on top of it, are integrated out. We claim that, in the small t Hooft coupling limit, the instanton is well described by a Skyrmion arising from the low energy effective Lagrangian of the Sakai-Sugimoto model. The sextic term plays a dominant role in this limit. Moreover, when a pion mass term is added we recover the BPS Skyrme model in the small t Hooft coupling limit.