Clinical pharmacologists face unique challenges when developing drugs for rare diseases. These conditions are characterized by small patient populations, diverse disease progression patterns, and a limited understanding of underlying pathophysiology. This tutorial serves as a comprehensive guide, offering practical insights and strategies to navigate its complexities. In this tutorial, we outline global regulatory incentives and resources available to support rare disease research, describe some considerations for designing a clinical development plan for rare diseases, and we highlight the role of biomarkers, real-world data, and modeling and simulations to navigate rare disease challenges. By leveraging these tools and understanding regulatory pathways, clinical pharmacologists can significantly contribute to advancing therapeutic options for rare diseases.