The objective of this paper is to investigate the uncertainty in the bondline temperature response of a flexible thermal protection system subject to uncertain parameters in the hypersonic flowfield and thermal response modeling of a hypersonic inflatable aerodynamic decelerator configuration for ballistic Mars entry. An inflatable decelerator with a 10 m major diameter is selected for this study based on the forebody dimensions scaled from the 6 m test article that was tested in the NASA Ames Research Center’s National Full-Scale Aerodynamics Complex facility. A global nonlinear sensitivity analysis study for the bondline temperature uncertainty shows that the dimension of uncertain parameters can reduce from 22 to 8. An uncertainty analysis of the bondline temperature in the reduced dimensions indicates that the bondline temperature varies by as much as 125% above the nominal prediction and exceeds the temperature limit of 400°C. The largest uncertainty occurred at 70 s in the trajectory before separation of the inflatable decelerator for transition to a secondary descent technology. The main contributors to the bondline temperature uncertainty are the insulator and outer fabric conductivities, as well as the freestream density. The thickness and initial density of the insulator layer, closest to the gas barrier layer, are also shown to be significant contributors to the bondline temperature uncertainty, especially earlier in the trajectory.