We report time- and angle-resolved photoemission spectroscopy measurements on the topological insulator Bi(2)Se(3). We observe oscillatory modulations of the electronic structure of both the bulk and surface states at a frequency of 2.23 THz due to coherent excitation of an A(1g) phonon mode. A distinct, additional frequency of 2.05 THz is observed in the surface state only. The lower phonon frequency at the surface is attributed to the termination of the crystal and thus reduction of interlayer van der Waals forces, which serve as restorative forces for out-of-plane lattice distortions. Density functional theory calculations quantitatively reproduce the magnitude of the surface phonon softening. These results represent the first band-resolved evidence of the A(1g) phonon mode coupling to the surface state in a topological insulator.