The steady-state assumption for catchment transit time is a controversial issue in catchment hydrology. In this study, we propose a new approach to estimate the time-variant mean transit time (MTT) and transit time distribution (TTD) using a five-layer tank model with isotopic tracers and test it in the Fuefuki River catchment, central Japan. Model parameters were optimized during the calibration phase based on hydrometric and isotopic observations and then validated in a separate validation phase. The long-term (2003–2012) average MTT was estimated to be 23.7 years. However, the daily MTT was highly variable, ranging from 1.2 to 37.0 years. Instantaneous TTD also varied markedly. Precipitation alters TTD by increasing younger components and shortens the MTT. Thus, a steady-state assumption is inappropriate, with the relationship between monthly MTT and precipitation amount most closely approximated by an exponential function. The dependence of MTT on precipitation is an important descriptor for characterizing catchments. Although optimized model-parameters have some uncertainties, potential errors in estimating the MTT are relatively small (e.g., < ±3 years). Therefore, the tracer-aided tank model is useful for estimating time variations in MTT and TTD with high reliability.