Objective To determine the effect of foot orthoses on pain, disability and foot functionality in patients with Systemic Lupus Erythematosus. Design Randomized clinical trial. Setting University Podiatric Clinical Area. Subjects Patients with systemic lupus erythematosus. Interventions Patients were randomly assigned to either group A, which received custom-made functional foot orthoses, or group B, which received flat cushioning insoles, for three months. Main measures The primary outcome was foot pain, measured by 11-point numeric pain rating scale. Foot functionality and foot-related disability were evaluated using the foot function index, the Manchester foot pain and disability, at the beginning and at days 90. Results Sixty-six participants (age 47.3 ± 11.9 years) suffering from foot pain, received either the custom-made foot orthoses ( N = 33) or the flat cushioning insoles ( N = 33). For the analysis of the data, only participants who had finished the follow-up period (90 days) were included. None statistically significant difference between groups were found. In group A, all variables showed statistically significant differences when comparing the initial and final measurements. Pain showed 6.8 ± 1.6 and 4.2 ± 2.9 in group A, at baseline and at 90 days, respectively, group B showed 6.5 ± 1.5 and 4.7 ± 3.0 at baseline and at 90 days, respectively. Conclusion Both groups showed a reduction in foot pain. This study suggests that not only controlling the foot function, but providing cushioning to the foot, may have positive effects to manage foot pain in patients with systemic lupus erythematosus.