Objective. To evaluate the efficacy of a 3-month exercise training program in counteracting the chronotropic incompetence and delayed heart rate recovery in patients with systemic lupus erythematosus (SLE). Methods. A 12-week randomized trial was conducted. Twenty-four inactive SLE patients were randomly assigned into 2 groups: trained (T; n ؍ 15, 3-month exercise program) and nontrained (NT; n ؍ 13). A sex-, body mass index-, and age-matched healthy control (C) group (n ؍ 8) also underwent the exercise program. Subjects were assessed at baseline and at 12 weeks after training. Main measurements included the chronotropic reserve (CR) and the heart rate (HR) recovery (⌬HRR) as defined by the difference between HR at peak exercise and at both the first (⌬HRR1) and second (⌬HRR2) minutes after the exercise test. Results. Neither the NT SLE patients nor the C group presented any change in the CR or in ⌬HRR1 and ⌬HRR2 (P > 0.05). The exercise training program was effective in promoting significant increases in CR (P ؍ 0.007, effect size [ES] 1.15) and in ⌬HRR1 and ⌬HRR2 (P ؍ 0.009, ES 1.12 and P ؍ 0.002, ES 1.11, respectively) in the SLE T group when compared with the NT group. Moreover, the HR response in SLE patients after training achieved parameters comparable to the C group, as evidenced by the analysis of variance and by the Z score analysis (P > 0.05, T versus C). Systemic Lupus Erythematosus Disease Activity Index scores remained stable throughout the study. Conclusion. A 3-month exercise training program was safe and capable of reducing the chronotropic incompetence and the delayed ⌬HRR observed in physically inactive SLE patients.