Background: Burns and their associated wound care procedures evoke significant stress and anxiety, particularly for children. Little is known about the body's physiological stress reactions throughout the stages of re-epithelialization following an acute burn injury. Previously, serum and urinary cortisol have been used to measure stress in burn patients, however these measures are not suitable for a pediatric burn outpatient setting. Aim: To assess the sensitivity of salivary cortisol and sAA in detecting stress during acute burn wound care procedures and to investigate the body's physiological stress reactions throughout burn re-epithelialization. Methods: Seventy-seven participants aged four to thirteen years who presented with an acute burn injury to the burn center at the Royal Children's Hospital, Brisbane, Australia, were recruited between August 2011 and August 2012. Results: Both biomarkers were responsive to the stress of burn wound care procedures. sAA levels were on average 50.2 U/ml higher (p < 0.001) at 10 min post-dressing removal compared to baseline levels. Salivary cortisol levels showed a blunted effect with average levels at ten minutes post dressing removal decreasing by 0.54 nmol/L (p < 0.001) compared to baseline levels. sAA levels were associated with pain (p = 0.021), no medication (p = 0.047) and Child Trauma Screening Questionnaire scores at three months post re-epithelialization (p = 0.008). Similarly, salivary cortisol was associated with no medication (p < 0.001), pain scores (p = 0.045) and total body surface area of the burn (p = 0.010). Conclusion: Factors which support the use of sAA over salivary cortisol to assess stress during morning acute burn wound care procedures include; sensitivity, morning clinic times relative to cortisol's diurnal peaks, and relative cost.