This study explores the relationship between perceived authenticity and cognitive engagement within authentic learning environments, a topic that has garnered increasing attention in educational research and practice. While previous studies have linked authenticity and engagement to improved academic outcomes, there remains a gap in understanding how specific dimensions of authenticity impact various aspects of learning engagement.To address this gap, this research investigates learners’ perceived authenticity, cognitive engagement, and their relationship across four distinct learning phases: reading, introductory video, virtual simulation, and debriefing. Employing a mixed-methods approach, the research combines functional near-infrared spectroscopy (fNIRS) to gather real-time physiological data with semi-structured interviews to capture participants' perceptions of authenticity and cognitive engagement. Three core research questions guided the study: (1) What are the levels of perceived authenticity across four learning phases? (2) What are the levels of cognitive engagement—both perceived and physiological—across these phases? (3) What is the relationship between perceived authenticity and cognitive engagement? The findings reveal significant findings in perceived authenticity and cognitive engagement. The virtual simulation phase, which incorporated all three dimensions of authentic learning, elicited the highest levels of both perceived and physiological engagement. The reading and debriefing phases also promoted higher engagement, though each emphasized different aspects of authentic learning. In contrast, the introductory video phase, perceived as the least authentic, generated the lowest engagement levels. Additionally, fNIRS measurements provided valuable information on cognitive engagement. Using Bland-Altman plots, the alignment analysis validated the congruence between participants' perceptions and physiological measurements, underscoring the reliability of combining both approaches to assess cognitive engagement comprehensively. Kendall’s Tau correlation analysis showed strong positive relationships between perceived authenticity and both perceived and physiological cognitive engagement (r(28) = 0.77, p = 0.001; r(38) = 0.76, p < 0.001). These findings highlight the importance of integrating comprehensive authentic learning activities to enhance learning engagement. In conclusion, this study provides valuable insights into the complex relationship between authenticity and cognitive engagement, offering evidence-based recommendations for designing authentic learning environments that effectively enhance learners' cognitive engagement, ultimately leading to improved academic performance.