We report in this Letter the outstanding frequency stability performance of an autonomous cryogenic sapphire oscillator (CSO) presenting a flicker frequency noise floor below 2×10−16 near 1000 s of integration time and a long-term Allan deviation limited by a random walk process of ∼1×10−18τ. The frequency stability qualification at this level called for the implementation of sophisticated instrumentation associated with ultra-stable frequency references. This result is technologically sound as it demonstrates the potentiality of the CSO technology. From the physical point of view, it sets an upper limit to the ultimate noise floor of the cryogenic microwave resonator that is competitive to that of the ultra-stable optical Fabry–Pérot cavities.