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. If confirmed, the new effect has to be taken into account, as the above direct $CP$ asymmetries are used to search for new physics.