Solar trackers are constructions consisting of a series of photovoltaic modules mounted on a motorized supporting structure; such systems are usually characterized by limited torsional stiffness and low number of torsional constraints, factors that lead to lower structural frequencies. At these frequencies, trackers are typically susceptible to turbulent wind, and when excited by it, the expected responses can lead to significant deformations and, with its cyclical load variation, also to fatigue damage. On this premise, the presented article proposes a methodology for estimating fatigue damage caused by dynamic wind effects in single-axis solar trackers. As observed in full-scale scenarios, it is assumed that the fatigue damage accumulates in correspondence of the elements connecting the photovoltaic modules to the underlying structure. To this end, a transfer function that relates the pressure acting on the panel to the stress state in a specific point is evaluated with a finite element (FE) model and then experimentally validated with a cyclical load test. Acting forces time histories, derived by wind tunnel measurements, are used with the transfer function to infer the evolution of the stresses acting in the regions of interest. Finally, the rainflow cycle count method is used in conjunction with the Wöhler curve of the investigated structural detail to analyze the stress history and derive a fatigue damage estimate. It is expected that the proposed approach can aid designers in the damage estimation and verification procedures.