(1) Background: Patients who undergo a medical rehabilitation treatment are often facing a physical, emotional and spiritual crisis, mostly due to pain, loss of limb functionality, the memory of the pre-disease days or questions about their role and value in life. Most of the time, the physician does not have the ability to deal with these issues or to provide the expected responses. The aim of this study was to analyze the patient’s perception on spirituality and faith while going through a medical rehabilitation program. (2) Methods: The current study included 173 patients treated in the Rehabilitation Department of the Clinical Rehabilitation Hospital in Cluj-Napoca, Romania. Of them, 91 comprised the study group and were assessed in 2023, while 82 comprised the control group and were assessed in 2007. All patients answered a 34-item questionnaire designed by the authors regarding the role of religion, spirituality and prayer in their post-disease life. (3) Results: The results show that 99% of the patients assessed believe in God, 80% pray every day, 50% have less pain after praying and 44% trust their priest the same as they trust their doctor. When comparing groups, results from 2023 show that more patients pray every day, while fewer are afraid of dying, think their disease is serious or wish for the medical team to pray with them, compared to 2007. (4) Conclusions: The physician should not neglect the faith of the patient and should use it to achieve a better rehabilitation outcome.