As higher education faces challenges in driving innovation, the effectiveness of academic leaders affects an institution’s overall performance. In Taiwan, most of the leading research focuses on leadership in primary and secondary schools. In this study, we interviewed a public university’s academic and administrative directors to outline the responsibilities and expectations of academic leaders, and investigated the problems and challenges that they faced during their work process to propose the support and leadership development needed for them to navigate through the obstacles and challenges. The results illustrate that an ideal academic leader should possess the following essential qualities and skills: enthusiasm, empathy, fairness and openness, and interpersonal communication skills. Academic leaders are faced with problems including budget, student enrollment, professors’ rights, and conflicts between professors and students, and challenges resulting from social change, such as faculty recruitment, student career development, university transformation and self-efficacy in administration. According to these findings, we propose suggestions for revising election procedures of institutional leaders and a leadership development program. The study contributes to this research field by offering insights of the problems and challenges of transiting from a faculty member to an administrator and by proposing a support system to enhance department leaders’ awareness of the importance of their roles and responsibilities in building consensus toward university development direction.