The 16-year-old male died of massive injuries to his liver despite two emergency surgeries that attempted to repair the damage.
The victim was injured in Isso, about 200 miles southeast of Madrid, where the bulls were being run as part of a festival for the town's patron saint.
Another man was injured in the leg during the run.
Britain's Sky News said bull runs are frequent parts of summer festivals around Spain.
Critics and supporters alike have agreed the safety standards are lax at best, allowing people to take part regardless of their physical fitness or sobriety status.