The thermochronological method was applied to metamorphic rocks distributed in eastern Nepal to elucidate the denudation process of the upper-crust of the continental collision zone. New results of systematic fission-track (FT) age dating and FT length measurements of zircon and apatite were utilized in the thermochronological inverse analysis to reconstruct the time-temperature (t-T) paths in the temperature range of 60–350°C. Eight t-T paths obtained along the across-strike section in eastern Nepal showed that the cooling process of the metamorphic rocks are characterized by 1) gradual cooling (<30°C/Myr) followed by rapid cooling (~150°C/Myr) and subsequent gradual cooling (gradual-rapid-gradual cooling: GRG cooling), 2) northward-younging of the timing of the rapid cooling since ca. 9 Ma. The observed FT ages and t-T paths were then compared with the FT ages and t-T paths obtained by forward calculations using 3-D thermokinematic models to test the following four tectono-thermal models which have been proposed in the Central and Eastern Himalayas: 1) The denudation of the upper-crust is associated with the movement of the plate boundary fault (Main Himalayan Thrust: MHT) showing flat geometry (the Flat MHT model) and 2) flat-ramp-flat geometry (the Flat-Ramp-Flat MHT model), 3) the denudation of the upper-crust is mainly controlled by the focused uplift associated with the growth of the Lesser Himalayan Duplex (the Duplex 01-03 model) or 4) slip of the splay fault of the MHT (the Splay Fault model). As a result, only the Flat-Ramp-Flat MHT model reconstructed similar t-T paths and age distribution patterns obtained from eastern Nepal. This suggests that the observed FT ages and t-T paths reflect a denudation process driven by the movement of the MHT showing a flat-ramp-flat geometry. The GRG cooling and the northward-younging of the timing of rapid cooling indicate that the flat-ramp-flat geometry of the MHT was established by ca. 9 Ma and has been stable thereafter. The result of the thermokinematic inverse analysis also indicates that the denudation rate and its spatial distribution have been stable since ca. 9 Ma.