The study examines the challenges of implementing instructional design in higher distance education and its impact on student learning, highlighting obstacles such as teacher resistance to change, the need for adequate technological resources, and adaptation to student diversity. Through a systematic literature review following the PRISMA protocol and using qualitative analysis, these obstacles are identified, and their effects on learning are examined, such as the development of essential 21st-century skills and knowledge retention. The findings emphasize the importance of a continuous culture of innovation, support for teachers, inclusive and personalized strategies to improve accessibility, and the need for a robust technological infrastructure. It concludes that overcoming these challenges requires a holistic and integrated approach, focused on the needs of both students and educators, to transform distance education into an inclusive, accessible, and conducive modality for educational innovation and transformation, thus preparing students to face the challenges of the modern world with adequate skills and knowledge.