This paper reviews the ethical tensions and the dual loyalty conflict between following military orders and professional codes of conduct. All competent patients have a right to refuse medical treatment. However, maintaining confidentiality is not an absolute right. In the military, a doctor may have a dual loyalty conflict between obeying military orders and following professional codes of practice. This can become exacerbated when a doctor in a military environment does not consider all the parties’ interests. This paper suggests that dual loyalty conflict in military healthcare practice in this environment is best managed via a discretionary ethic-role. This then allows independent clinical judgment while at the same time minimizing ethical dilemmas, harm, and conflict to a third party such as a military commander.