This study explored the ethical judgment process of employee assistance program (EAPs) professionals on confidentiality issues. In-depth interviews were conducted with six EAPs professionals within the company, and the “category content” strategy was used for conducting qualitative analysis in the narrative study. The study found that EAPs professionals within the company have different types of confidentiality issues and experience the conflict, judgment, and impact stages of the ethical judgment process. First, the following confidentiality issues are encountered in the conflict stage: (1) the involvement of administrative forces in the operation of EAPs, thus leading to a confidentiality dilemma, (2) the differences in the attitudes of the parties toward the perception of confidentiality, and (3) the conflicts in the consideration of the confidential exception and the duty to warn. Second, in the judgment stage, EAPs professionals within the company make ethical judgments and decisions based on five aspects: (1) by using the EAPs code of ethics, (2) by considering whether the rights of the client are harmed, (3) by considering the optimal welfare of the client, (4) by evaluating and initiating related resource assistance, and (5) by considering the informed consent aspect in the decision for the parties. Third, in the impact stage, EAPs professionals within the company seek support from the support system and develop their adjustment methods: (1) internal self-adjustment, (2) inquiry pertaining to the external support system assistance, (3) redefining of the EAPs service function, (4) adjustment and coping strategies, and others. These processes will continue to precipitate and reflect, gradually forming the next treatment experience and judgment of ethical conflict events. Finally, based on the research results, this study also proposed relevant suggestions for the practical development of EAPs and the future research of the ethical issues of these programs.