A separately-designable diplexer with multiple transmission zeroes (TZs) using common stub-loaded stepped impedance resonator (SIR) is proposed. The common stub-loaded SIR operating in third harmonic (f3) and fifth harmonic (f5) is used for designing the two diplexer channels. The stub is loaded at the voltage-null point of f3 of the SIR. It can separately control f5 but has no effect on f3 so that the two channels can be separately designed. Meanwhile, the input port is tap-connected to the common stub-loaded SIR, which necessarily produces a TZ between f3 and f5, existing in both channel filtering responses. By properly choosing coupling schemes of the two channels, more TZs are realized at the desired locations. Thanks to the generation of the multiple TZs, both passband selectivity and isolation between the two channels are improved significantly. For demonstration, a diplexer operating at 2.22 and 2.95 GHz is designed, fabricated, and measured. The simulated and measured results are presented, showing good agreement.