Background: The difficulties encountered in practicing anatomy, physiology, and histology are examined in this paper. It is important to comprehend these challenges in order to enhance medical education and practice in Pakistan. Objectives: The aim of this study is to evaluate and determine the main problems that impact anatomy, physiology, and histology teaching and practice, and to provide practical ways to solve these problems. Methods: 132 faculty members participated in quantitative surveys, 20 important stakeholders participated in qualitative interviews, and departmental records and budgets were reviewed as part of a mixed-methods approach. The period of data collecting was January 2024–July 2024. Results: According to the survey, 65% of participants mentioned a lack of possibilities for professional growth, 70% mentioned insufficient money, and 78% of respondents said they had insufficient access to contemporary diagnostic equipment. Fifty percent of the participants voiced concerns over outdated courses, and sixty percent said they were overworked. These problems were validated by document evaluations, which also revealed large equipment deficiencies, out-of-date curriculum, and insufficient funding for anatomy, physiology, and histology.