Mechanical testing at small length scales has traditionally been resource-intensive due to difficulties with meticulous sample preparation, exacting load alignments, and precision measurements. Microscale fatigue testing can be particularly challenging due to the time-intensive, tedious repetition of single fatigue experiments. To mitigate these challenges, this work presents a new methodology for the high-throughput fatigue testing of thin films at the microscale. This methodology features a microelectromechanical systems-based Si carrier that can support the simultaneous and independent fatigue testing of an array of samples. To demonstrate this new technique, the microscale fatigue behavior of nanocrystalline Al is efficiently characterized via this Si carrier and automated fatigue testing with in situ scanning electron microscopy. This methodology reduces the total testing time by an order of magnitude, and the high-throughput fatigue results highlight the stochastic nature of the microscale fatigue response. This manuscript also discusses how this initial capability can be adapted to accommodate more samples, different materials, new geometries, and other loading modes.