We find a new $CP$-violation effect in charm decays into neutral kaons, which results from the interference between two tree (Cabibbo-favored and doubly Cabibbo-suppressed) amplitudes with the mixing of final-state mesons. This effect, estimated to be of order of $10^{-3}$, is much larger than the direct $CP$ asymmetries in these decays, but missed in the literature. It can be revealed by measuring the difference of the time-dependent $CP$ asymmetries in the $D^{+}\to \pi^{+}K_S^0$ and $D_{s}^{+}\to K^{+} K_S^0$ modes, which are accessible at the LHCb and Belle II. If confirmed, the new effect has to be taken into account, as the above direct $CP$ asymmetries are used to search for new physics.