The theoretical cornerstone of statistical mechanics is the ergodic assumption, i.e. the assumption that the time average of an observable equals its ensemble average. Here, we show how such a property is present when an open quantum system is continuously perturbed by an external environment effectively observing the system at random times while the system dynamics approaches the quantum Zeno regime. In this context, by large deviation theory we analytically show how the most probable value of the probability for the system to be in a given state eventually deviates from the non-stochastic case when the Zeno condition is not satisfied. We experimentally test our results with ultra-cold atoms prepared on an atom chip.