The job demands-resources model (JD-R) has shown an ability to predict worker engagement and exhaustion, yet to our knowledge, research has not been conducted that assesses the JD-R model with physiological indicators of chronic stress and burnout. Using the JD-R model, we assessed if occupational stress and burnout were related to dysregulated cortisol and salivary alpha-amylase awakening responses (sAA-AR). Professional apprentice jockeys comprising of males (n = 14) and females (n = 18) provided morning saliva samples and completed self-report measures relating to job demands and resources, burnout, and perceived mental and physical health. Data was collected at two time points coinciding with naturally occurring 'low' and 'high' stress periods during the racing calendar. The jockeys reported good physical and mental health but had elevated levels of the burnout subtypes cynicism and exhaustion. Regression analyses suggested that those jockeys presenting with reduced professional efficacy in the high stress period produced a 'flattened' sAA-AR indicative of reduced autonomic nervous system (ANS) arousal, which has been associated with burnout. Further, decreases in professional efficacy explained the relationship between increased workplace stress and decreased ANS activity in the high stress period. Our findings suggest that assessments of psychological stress or physiology in isolation are not as useful as looking at both in combination, and extend previous findings on the sAA-AR.