We conducted a case study to examine the challenges encountered in large-scale agile development (LSAD) within two Swedish software companies. While agile methodologies have proven successful in small and medium-sized projects, their implementation in large-scale software development projects can be problematic. To identify these challenges, we employed thematic analysis, which revealed a total of 26 distinct challenges. These challenges were categorized into three main themes: Processes and practices, Teams, and Organizational-level challenges in LSAD. By recognizing and addressing these challenges, projects operating in similar contexts can synchronize their activities and harness the advantages of agile methodologies at a large scale. The article delves into comprehensive discussions on these challenges, offering valuable insights and directions for future research endeavors.