An approach to the short range part of baryon-baryon interaction based on a non-relativistic quark model, proposed and formulated in the previous paper, is applied to the case of S-wave relative motion. Repulsive core like interactions appear in most of the spin(S)-isospin(T) states, including the NN system with (S, T) = (1, 0) and (0, 1), while attractive interactions are predicted for the ΔΔ system with (S, T) = (3, 0) and (1, 0). The interaction is mostly due to the Pauli principle between quarks and the spin-spin term in the quark-quark force, and is insensitive to the confinement term. The effect of meson exchanges, which is not included in the present non-relativistic quark model, is studied by simulating it with a phenomenological local potential. Qualitative behaviours of the S-wave NN phase shifts are reproduced in this way.