Background: Ethical issues in the patient-doctor relationship are central to the quality of healthcare delivery, particularly in clinical environments where communication, consent, privacy, and trust are fundamental. In Pakistan, where resource constraints and cultural complexities influence clinical practice, understanding ethical dynamics from both patient and physician perspectives is essential. Despite growing attention to medical ethics, there remains a lack of in-depth exploration of how ethical boundaries and dilemmas are experienced on both sides of the therapeutic relationship. Objectives: This qualitative study aimed to (1) explore the ethical challenges and moral dilemmas experienced by healthcare professionals in maintaining professional boundaries within the patient-doctor relationship; (2) understand patients’ perspectives on ethical concerns such as communication, informed consent, privacy, and decision-making; and (3) identify areas of ethical conflict or misalignment between patients and doctors, and examine their impact on trust and therapeutic alliance. Methods: Using a qualitative exploratory design, in-depth semi-structured interviews were conducted with 26 participants (13 medical doctors and 13 adult patients) recruited through purposive and snowball sampling. Inclusion criteria ensured participants had sufficient clinical experience (for doctors) or recent consultation experiences (for patients). Thematic Analysis was employed following Braun and Clarke’s six-step framework to interpret the data. Results: Six major themes emerged: (1) Communication Gaps and Ethical Misunderstandings, (2) Professional Boundaries, (3) Trust and Confidentiality, (4) Ethical Stress and Moral Conflict in Practice, (5) Ethical Perception and Standards, and (6) Reciprocal Ethical Violations and Breaches of Conduct. Participants described challenges such as emotional disengagement, institutional constraints, rushed consent procedures, physical and sexual misconduct, and divergent ethical expectations, all of which affected the therapeutic alliance. Conclusion: The study revealed that ethical breaches are not unidirectional; misconduct can originate from both parties. Doctors often experience verbal abuse, false accusations, and harassment from patients or their attendants, while patients report instances of neglect, inadequate consent, and lack of empathy. These reciprocal violations, when compounded by systemic challenges such as resource constraints, poor governance, and institutional neglect, deepen the moral distress on both sides and erode trust in the clinical relationship. Addressing these challenges requires not only stronger ethical training for practitioners but also public awareness campaigns that promote patient responsibilities, respectful conduct, and constructive dialogue within the healthcare system. Ethical reform, therefore, must be relational, inclusive, and context-sensitive, acknowledging the lived experiences of both patients and doctors. Promoting mutual respect, emotional sensitivity, and ethical accountability is crucial for improving healthcare experiences and outcomes.