This study examined the impact of custom foot orthoses made of ethyl-vinyl acetate (EVA) and expanded thermoplastic polyurethane (TPU) materials, both compared to a control condition (CON; shoes only), on mechanical asymmetries during repeated treadmill sprints. Eighteen well-trained male runners executed eight, 5-s sprints (rest: 25 s) on an instrumented motorized treadmill in three footwear conditions (EVA, TPU, and CON). We evaluated the group mean asymmetry scores using the ‘symmetry angle’ (SA) formula, which assigns a score of 0% for perfect symmetry and a score of 100% for perfect asymmetry. There was no condition (all p ≥ 0.053) or time (p ≥ 0.074) main effects, nor were there any significant time × condition interactions on SA scores for any variables (p ≥ 0.640). Mean vertical, horizontal, and total forces presented mean SA values (pooled values for the three conditions) of 2.6 ± 1.9%, 2.9 ± 1.6%, and 2.4 ± 1.8%, respectively. Mean SA scores were ~1–3% for contact time (1.5 ± 0.5%), flight time (3.0 ± 0.3%), step frequency (1.1 ± 0.5%), step length (1.9 ± 0.7%), vertical stiffness (2.1 ± 0.9%), and leg stiffness (2.4 ± 1.1%). Mean SA scores were ~2–6.5% for duration of braking (4.1 ± 1.6%) and propulsive (2.4 ± 1.0%) phases, and peak braking (6.2 ± 2.9%) and propulsive (2.1 ± 1.4%) forces. In well-trained runners facing intense fatigue, wearing custom foot orthoses did not modify the observed low-to-moderate natural stride mechanical asymmetries.