We develop a scheme for the computation of the full-counting statistics of transport described by Markovian master equations with an arbitrary time dependence. It is based on a hierarchy of generalized density operators, where the trace of each operator yields one cumulant. This direct relation offers a better numerical efficiency than the equivalent number-resolved master equation. The proposed method is particularly useful for conductors with an elaborate time dependence stemming, e.g., from pulses or combinations of slow and fast parameter switching. As a test bench for the evaluation of the numerical stability, we consider time-independent problems for which the full-counting statistics can be computed by other means. As applications, we study cumulants of higher order for two time-dependent transport problems of recent interest, namely steady-state coherent transfer by adiabatic passage (CTAP) and Landau-Zener-Stückelberg-Majorana (LZSM) interference in an open double quantum dot.