Certifying quantum measurements is increasingly important for foundational insights in quantum information science. Here, we report an experimental certification of unknown quantum measurements in a semi-device-independent setting. For the first time, we experimentally demonstrate that genuine three-outcome positive operator-valued measures (POVMs) can be certified under the assumption of a limited overlap between the prepared quantum states. The generalized quantum measurements are realized through discrete-time quantum walk and our experimental results clearly show that three-outcome POVMs can be certified even in the presence of noise. Finally, we experimentally investigate that optimal POVMs for performing unambiguous state discrimination can be self-tested. Our work opens new avenues for robust certification of quantum systems in the prepare-and-measure scenario.