A growing body of work has established the modeling of stochastic processes as a promising area of application for quantum technologies; it has been shown that quantum models are able to replicate the future statistics of a stochastic process while retaining less information about the past than any classical model must, even for a purely classical process. Such memory-efficient models open a potential future route to study complex systems in greater detail than ever before and suggest profound consequences for our notions of structure in their dynamics. Yet, to date methods for constructing these quantum models are based on having a prior knowledge of the optimal classical model. Here, we introduce a protocol for blind inference of the memory structure of quantum models—tailored to take advantage of quantum features—direct from time-series data, in the process highlighting the robustness of their structure to noise. This in turn provides a way to construct memory-efficient quantum models of stochastic processes while circumventing certain drawbacks that manifest solely as a result of classical information processing in classical inference protocols.