We find a new $CP$ violating effect in charmed hadron decays into neutral kaons, which is induced by the interference between the Cabibbo-favored and doubly Cabibbo-suppressed amplitudes with the $K^{0}-\overline K^{0}$ mixing. It is estimated to be of order of $\mathcal{O}(10^{-3})$, much larger than the direct $CP$ asymmetry, but missed in the literature. To reveal this new $CP$ violation effect, we propose a new observable,
the difference of the $CP$ asymmetries in the
$D^{+}\to \pi^{+}K_S^0$ and $D_{s}^{+}\to K^{+} K_S^0$ modes.
Once the new effect is determined by experiments, the direct $CP$ asymmetry then can be extracted and used to search for new physics.