A problem of robust fault diagnosis of digital controlled continuous-time systems with uncertain time-varying input delay is studied in this paper. Two residual-based fault detection and isolation (FDI) schemes are proposed that are robust in terms of time-varying delays induced by the electronic devices and disturbances. The idea of both proposed methods is to transform the uncertainty caused by delays into unknown inputs and decouple them by means of eigenstructure assignment (EA) technique. The first method utilizes a Cayley-Hamilton theorem based transformation and the second relies on a first order Pad'e approximation of the time delay. Finally, the applicability and effectiveness of the proposed methods is illustrated through simulation results from the "high-fidelity" industrial simulator, provided by Thales Alenia Space.