Background: People with multiple sclerosis (PwMS) suffer from some comorbidities, including physical and psychiatric disorders, low quality of life (QoL), hormonal dysregulation, and hypothalamic-pituitary-adrenal axis dysfunction. The current study aimed to investigate the effects of eight weeks of tele-yoga and tele-Pilates on the serum levels of prolactin and cortisol and selected physical and psychological factors. Methods: Forty-five females with relapsing remitting multiple sclerosis, based on age (18–65), expanded disability status scale (0–5.5), and body mass index (20–32), were randomly assigned to tele-Pilates, tele-yoga, or control groups (n = 15). Serum blood samples and validated questionnaires were collected before and after interventions. Results: Following online interventions, there was a significant increase in the serum levels of prolactin (p = 0.004) and a significant decrease in cortisol (p = 0.04) in the time × group interaction factors. In addition, significant improvements were observed in depression (p = 0.001), physical activity levels (p < 0.001), QoL (p ≤ 0.001), and the speed of walking (p < 0.001). Conclusion: Our findings suggest that tele-yoga and tele-Pilates training could be introduced as patient-friendly, non-pharmacological, add-on therapeutic methods for increasing prolactin and decreasing cortisol serum levels and achieving clinically relevant improvements in depression, walking speed, physical activity level, and QoL in female MS patients.