The generalised Sakai-Sugimoto model consists of the $N_c$ colour D4-branes as a background and the $N_f$ probe flavour D8-branes whose separation at UV limit is denoted by $l$. One can incorporate into this model the baryons which are represented by the D4-branes wrapping $S^4$. We consider the chiral condensate given by an open Wilson line in this model with baryon density. Evaluating the vev of open Wilson line holographically, we clarify the density dependence of chiral condensate and its relation with that of chiral symmetry breaking/restoration. We also study how the chiral condensate behaves by changing $l$, the parameter of the model.