Increased cardiovascular morbidity and mortality rates for patients with schizophrenia are reported to contribute to their reduced life expectancy. Common reasons for increased cardiac mortality rates include cigarette smoking, obesity, dyslipidemia, diabetes, and poorer health behavior in general. The majority of excess mortality among people with schizophrenia is caused by cardiovascular complications. Reduced vagal activity might be one important mechanism leading to this increased cardiac mortality and has been consistently described in patients and their healthy first-degree relatives. In this case study, we compared two different aerobic exercise regimes in one patient with chronic schizophrenia to investigate their effects on cardiovascular regulation. The patient completed a 6-week period of moderate continuous training (CT) followed by a 6-week period of interval training (IT), each regime two times per week, on a stationary bicycle. This was followed by a 6-week period of detraining. Primary outcome measures examined heart rate (HR) and heart rate variability (HRV) at rest while secondary measures assessed fitness parameters such as the ventilatory threshold 1 (VT1). We observed that IT was far more effective than moderate CT in increasing HRV, as indicated by root mean of squared successive difference (improvement to baseline 27 versus 18%), and reducing resting HR (-14 versus 0%). Improvement in VT1 (21 versus -1%) was only observed after IT. Our study provides preliminary data that the type of intervention is highly influential for improving cardiac function in patients with schizophrenia. While cardiovascular function might be influenced by CT to some degree, no such effect was present in this patient with schizophrenia. In addition, the beneficial effect of IT on HR regulation vanished completely after a very short period of detraining after the intervention.