Background: Calcaneal apophysitis (Sever disease) is a benign ailment which causes heel pain in children. Conservative treatment strategies are widely popular and the prescription of prefabricated orthoses and heel-lifts is very widespread. The aim of the present research was to determine the effectiveness to relieve calcaneal apophysitis pain using “off-the-shelf” heel-lifts and custom-made orthotics. Methods: Two intervention modalities were evaluated and compared in a 12-week follow-up randomized comparative effectiveness trial. Inclusion criteria included 9 to 12 years old boys or girls diagnosed of calcaneal apophysitis, primary exclusion criteria included children who had suffered from foot trauma on the heel or had received previous treatment. Children were stratified randomized into experimental (custom-made polypropylene foot orthoses) and control (“off-the-shelf” heel-lifts) group. The primary outcome was calcaneal apophysitis pain perception, which was assessed by the Visual Analogical Scale (VAS), the algometry threshold and the Sport Activity Pain perception. Points of measure were at baseline and after the follow-up period. Analysis was performed according to the intention-to treat principles.Results: A total of 208 patients were included. Overall, 9 patients were lost to follow-up. Experimental group showed an increase in threshold algometry by 53.4% (95% CI 47.1% to 59.7%), a decrease in VAS by -68.6% (95% CI -74.5% to -62.7%) and a 20.8 times higher probability of improvement of Sport Activity (95% CI 8.9 to 48.6), compared with control group (p <0.001).Conclusions: Calcaneal apophysitis pain perception was improved in both groups custom-made foot orthoses and heel-lifts, but the experimental group revealed significant changes compared with control group. Children who used custom-made foot orthoses had greater probabilities to improve. Physicians should consider these findings in order to prescribe the most effective treatment in the approach of the calcaneal apophysitis. Trial registration: ClinicalTrials.gov Identifier: NCT03960086.