Background: Schoolchildren often spend a lot of time carrying a backpack with school equipment, which can be very heavy. The impact a backpack may have on the pronated feet of schoolchildren is unknown. Aims: The objective of this study was to evaluate the association of the backpack use on static foot posture in schoolchildren with a pronated foot posture over 36 months of follow-up. Methods: This observational longitudinal prospective study was based on a cohort of consecutive healthy schoolchildren with pronated feet from fifteen different schools in Plasencia (Spain). The following parameters were collected and measured in all children included in the study: sex, age, height, weight, body mass index, metatarsal formula, foot shape, type of shoes, and type of schoolbag (non-backpack and backpack). Static foot posture was determined by the mean of the foot posture index (FPI). The FPI was assessed again after 36 months. Results: A total of 112 participants used a backpack when going to school. Over the 36-month follow-up period, 76 schoolchildren who had a static pronated foot posture evolve a neutral foot posture. Univariate analysis showed that the schoolchildren using backpacks were at a greater risk of not developing neutral foot (odds ratio [OR]: 2.09; 95% CI: 1.08–4.09). The multivariate analysis provided similar results, where the schoolchildren using a backpack (adjusted OR [aOR]: 1.94; 95% CI: 1.02–3.82) had a significantly greater risk of not developing a neutral foot posture. Conclusions: A weak relationship was found between backpack use and schoolchildren aged from five to eleven years with static pronated feet not developing a neutral foot posture over a follow-up period of 36 months.