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This study examined the effects of minimal, maximal and conventional running footwear on tibial strains and stress fracture probability using finite element and probabilistic analyses. The current investigation examined fifteen males running in three footwear conditions (minimal, maximal and conventional). Kinematic data were collected during overground running at 4.0 m/s using an eight-camera motion-capture system and ground reaction forces using a force plate. Tibial strains were quantified using finite element modelling and stress fracture probability calculated via probabilistic modelling over 100 days of running. Ninetieth percentile tibial strains were significantly greater in minimal (4681.13 με) (p < 0.001) and conventional (4498.84 με) (p = 0.007) footwear compared to maximal (4069.65 με). Furthermore, tibial stress fracture probability was significantly greater in minimal footwear (0.22) (p = 0.047) compared to maximal (0.15). The observations from this investigation show that compared to minimal footwear, maximal running shoes appear to be effective in attenuating runners’ likelihood of developing a tibial stress fracture.