In conventional solid-state systems, the development of an energy gap is often associated with a broken symmetry. However, strongly correlated materials can exhibit energy gaps without any global symmetry breaking -- the so-called pseudogap, most notably in the Mott insulating state1 and the fluctuating superconducting or charge density wave states. To date, lattice induced pseudogap remains elusive. With angle-resolved photoemission spectroscopy (ARPES) and single crystal x-ray diffraction, we identify a pseudogap in the quasi-1D excitonic insulator candidate Ta2NiSe5. Strong lattice contribution is revealed by the pervasive diffuse scattering well above the transition temperature and the negative electronic compressibility in the pseudogap state. Combining first-principles and microscopic model calculations, we show that inter-band electron-phonon coupling can create fluctuating phonon-mediated electron-hole pairing or hybridization. This suppresses the spectral weight on the Fermi surface, causing a metal-to-insulator-like transition without breaking the global symmetry. Our work establishes the precedence of a pseudogap with a lattice origin, highlighting Ta2NiSe5 as a room-temperature platform to study lattice-induced charge localization and low dimensional fluctuations.