Purpose: Many patients with acute coronary syndrome experience problematic or altered sexual function. This aspect of the disease is frequently ignored or overlooked by the healthcare community even though it can strongly influence health-related patient quality of life (HRQoL). Thus, the aim of this study was to compare the effects of a specific cardiac rehabilitation programme focused on aerobic and neuromuscular strength-resistance training to those of a classic rehabilitation programme, both in terms of HRQoL and erectile dysfunction in patients with acute coronary syndrome. Methods: This study reports both secondary and unregistered outcomes from a double-blinded, randomised, and controlled clinical trial. The proposed intervention was based on the completion of a 20-session (10-week) cardiac rehabilitation programme for patients with cardiovascular disease. The patient cohort had been diagnosed with acute coronary syndrome and was recruited at the Cardiology Service of a private tertiary hospital. The outcomes assessed in this study were HRQoL and erectile disfunction assessed at baseline, after the intervention, and at a 6-month follow-up. Results: A total of 30 participants were randomly allocated to each study arm. The results of the two-way mixed ANOVAs showed significant group × time interactions for all the outcome measures (EQ-5D_index, p = 0.004; EQ-5D_VAS, p = 0.017; QLMI-Q, p ≤ 0.001; and IIEF-5, p = 0.001). Conclusion: The neuromuscular strength training programme was more effective than the classic strength training programme in terms of increasing the HRQoL and improving erectile dysfunction in patients following acute coronary syndrome, with differences still remaining between these groups at the 6-month follow-up.