Blended learning is a pedagogical approach that combines face-to-face instruction with online activities and has garnered significant interest in recent years. Despite the potential benefits of blended learning, it faces several critical issues that may dampen stakeholders' enthusiasm within universities. Consequently, the current study explores the key challenges of blended learning in higher education institutions. The data for this research were collected through a qualitative approach, using a descriptive phenomenological method and semi-structured interviews with experts in the field. The findings were then analyzed using Colaizzi’s (1978) seven-step method. During our research, interviews were conducted with 14 experts in the field through purposeful sampling. From these comprehensive discussions, a total of 112 significant statements were identified. These statements were then meticulously categorized into ten initial themes, providing a structured overview of the data. Further analysis allowed us to distill the challenges associated with the blended learning approach in higher education into three critical factors. The validity of the qualitative data, based on the four criteria of Lincoln and Guba (1985)—credibility, transferability, dependability, and confirmability—was examined through re-coding by two independent coders and confirmed. The findings reveal that the challenges associated with implementing blended learning in higher education can be categorized into personal, organizational, and support-related factors. Each of these dimensions encompasses various critical elements. Notably, these research outcomes hold significant potential for facilitating the successful adoption of a pragmatic blended teaching and learning approach within higher education.