We investigate the von-Neumann entanglement entropy and Schmidt gap in the vortex-free ground state of the Kitaev model on the honeycomb lattice for square/rectangular and cylindrical subsystems. We find that, for both the subsystems, the free-fermionic contribution to the entanglement entropy SE exhibits signatures of the phase transitions between the gapless and gapped phases. However within the gapless phase, we find that SE does not show an expected monotonic behaviour as a function of the coupling Jz between the suitably defined one-dimensional chains for either geometry; moreover the system generically reaches a point of minimum entanglement within the gapless phase before the entanglement saturates or increases again until the gapped phase is reached. This may be attributed to the onset of gapless modes in the bulk spectrum and the competition between the correlation functions along various bonds. In the gapped phase, on the other hand, SE always monotonically varies with Jz independent of the sub-region size or shape. Finally, further confirming the Li-Haldane conjecture, we find that the Schmidt gap ∆ defined from the entanglement spectrum also signals the topological transitions but only if there are corresponding zero energy Majorana edge states that simultaneously appear or disappear across the transitions. We analytically corroborate some of our results on entanglement entropy, Schmidt gap, and the bulk-edge correspondence using perturbation theory.