We propose and analyze a sample-efficient protocol to estimate the fidelity between an experimentally prepared state and an ideal target state, applicable to a wide class of analog quantum simulators without advanced sophisticated spatiotemporal control. Our approach utilizes newly discovered universal fluctuations emerging from generic Hamiltonian dynamics, and it does not require any fine-tuned control over state preparation, quantum evolution, or readout capability. It only needs a small number of experimental measurements, achieving near optimal sample complexity: in ideal cases, a percent-level precision is obtained with $\sim 10^3$ measurements independent of system size. Furthermore, the accuracy of our fidelity estimation improves with increasing system size. We numerically demonstrate our protocol for a variety of quantum simulator platforms such as itinerant particles on optical lattices, trapped ions, and Rydberg atoms. We discuss further applications of our method for advanced tasks such as multi-parameter estimation of quantum states and processes.

7+27 pages, 3+9 figures v2: version accepted in Physical Review Letters