We propose a general and experimentally accessible framework to quantify transition timing in discrete quantum systems via the time-of-flow (TF) distribution. Defined from the rate of population change in a target state, the TF distribution can be reconstructed through repeated projective measurements at discrete times on independently prepared systems, thus avoiding Zeno inhibition. In monotonic regimes, it admits a clear interpretation as a time-of-arrival (TOA) or time-of-departure (TOD) distribution. We apply this approach to optimize time-dependent Hamiltonians, analyze shortcut-to-adiabaticity (STA) protocols, study non-adiabatic features in the dynamics of a three-level time-dependent detuning model, and derive a transition-based quantum speed limit (TF-QSL) for both closed and open quantum systems. We also establish a lower bound on temporal uncertainty and examine decoherence effects, demonstrating the versatility of the TF framework for quantum control and diagnostics. This method provides both a conceptual tool and an experimental protocol for probing and engineering quantum dynamics in discrete-state platforms.