Malaria is the dominant communicable disease in Ghana and is responsible for about forty percent of outpatient cases in health care facilities. Access to good quality health care is thus important to ensure good health status of the general population. The health facilities of the Ghanaian health care system are categorized into teaching, regional, and district hospitals as well as policlinics and health center. This study compares the quality of services provided by health facilities according to geographical location, and the type of facility providing the service. Quality indicators used included doctor shortage, waiting period, clarity of communication, and effectiveness of treatment. The results show that there are statistically significant variations in quality across regions as well as the type of facility regardless of patient, characteristics such as education, age, and occupation. Teaching hospitals provided the most effective treatment with high equity while the regional hospitals performed worse than district hospitals. Low effectiveness of treatment implies that the parasites remain in the blood stream and so further infection to others continues and incidence remains high. Recommendations are made to improve effectiveness of treatment and reduce variation.