Purpose: In recent years a sub-group of minimalist runners have emerged who aim to perform physical exercise more naturally in an attempt to reduce running-related injuries. Here we aimed to determine the effect that running with minimalist footwear in a prolonged run has on foot-impact accelerations. Method: Seventeen runners ran with minimalist and conventional shoes (MS and CS, respectively) in two separate sessions; the participants had experience with both footwear types. We measured the length and frequency of each stride, as well as the tibial and head impact acceleration every 5 minutes during a prolonged run (30 minutes at 80% of each individual's maximum aerobic speed). Results: There were significant differences in the acceleration rate in the tibia (CS: 516.1 ± 238.47 G/s and MS: 786.6 ± 238.45 G/s; p = 0.009) and head (CS: 73.3 ± 23.65 G/s and MS: 120.7 ± 44.13 G/s; p = 0.000). Our data indicate that the type of footwear increased the stride frequency and decreased length and that the impact acceleration is increased with MS compared to CS (p < 0.05 in both cases). However, the effect of prolonged run was not significantly different between CS and MS (p < 0.05). Conclusions: The peak tibia acceleration and headtibia acceleration rate indicate that the use of MS may be related to a higher risk of injury. These differences remained independently of the runners' fatigue state.