Recent angle-resolved spectroscopy in BiS$_2$-based superconductors has indicated that the superconducting gap amplitude possesses remarkable anisotropy and/or a sign change on a small Fermi pocket around $X$ point. It implies a possibility of an unconventional pairing state. Here we study the gap anisotropy in superconductivity mediated by inherent charge/quadrupole fluctuations in an extended Hubbard model, which includes inter-site interaction between Bi and S atoms. The first-principles downfolded band structure is composed of Bi $6p_x/p_y$ and S $3p_x/p_y$ orbitals on a BiS$_2$ single layer. Evaluating the linearized gap equation, we find that the ferroic charge/quadrupole fluctuation driven by the inter-site interaction leads to a fully-gapped $d_{x^2-y^2}$-wave pairing state, in which the gap amplitude has sizable anisotropy on the Fermi surface.