We study the validity of the fluctuation-dissipation theorem for an isolated quantum system of harmonically trapped dipolar molecules taken out of equilibrium by means of a quench, a sudden change in the Hamiltonian parameters. We find that the integrability of the system plays a crucial role in the validity of the fluctuation-dissipation theorem. Namely, the system thermalizes according to the eigenstate thermalization hypothesis and the theorem holds if the system is nonintegrable after the quench. However, it fails if the system is integrable, unless the initial state is an eigenstate of a nonintegrable Hamiltonian, in which case the system still thermalizes despite the eigenstate thermalization hypothesis failing to describe it.