Density functional theory (DFT) together with Car-Parrinello ab initio molecular dynamics (CP-AIMD) simulation has been used to investigate the free energy profiles of two representative S(N)2 reactions: (A) Cl-+CH3Cl-->ClCH3+Cl-; (B) NH3+H3BNH3-->H3NBH3+NH3. The free energy profiles along the reaction coordinates at 300 K and 600 K were determined directly by a pointwise thermodynamic integration (PTI) technique. Comparison between the well-known double-well potential energy profile (PEP) and the free energy profiles (FEP) has been made. The results show that, for reaction A, the double-well profile is maintained for the FEP at 300 K due to the stronger ion-dipole interaction between chloromethane and the chloride anion. In comparison with the PEP, the FEP has a higher central barrier and a more shallow well depth. However, at 600 K the double wells almost disappear on the FEP, whereas the central barrier increases further. For reaction B, the 300 K FEP also presents a higher central barrier peak and a more shallow well depth compared to the PEP. However, when the temperature increases to 600 K, a saddle shape FEP is obtained, which indicates that the reaction has changed mechanism from an associative S(N)2 reaction to a dissociative S(N)1 reaction. This change is driven by entropy.