Exceptional degeneracies and generically complex spectra of non-Hermitian systems are at the heart of numerous phenomena absent in the Hermitian realm. Recently, it was suggested that Floquet dissipative coupling in the space-time domain may provide a novel mechanism to drive intriguing spectral topology with no static analogs, though its experimental investigation in quantum systems remains elusive. We demonstrate such Floquet dissipative coupling in an ensemble of thermal atoms interacting with two spatially separated optical beams, and observe an anomalous anti-parity-time symmetry phase transition at an exception point far from the phase-transition threshold of the static counterpart. Our protocol sets the stage for Floquet engineering of non-Hermitian topological spectra, and for engineering new quantum phases that cannot exist in static systems.