Burn injury is a highly traumatic event for children and their families. The degree of burn severity (superficial-, deep-, or full-thickness injury) dictates the clinical management of the injury and the extent of scar formation. It can often take several days for the true depth of a burn injury to become apparent. Additionally, the biological processes by which burn injuries continue to develop and worsen over days or weeks (burn wound conversion) are not well understood. Burn blister fluid (BF), which develops after injury, contains proteins that reflect both the systemic and local microenvironment response to the injury and have the potential to diagnose burn wound severity. BF is collected non-invasively and therefore, it is ideal for studying the burn wound proteome in paediatric patients. BF samples were collected from 65 children in Brisbane (Queensland, Australia) and quantitatively analysed using SWATH mass spectrometry. An integrated peptide ion library, consisting of data-dependent analysis (DDA) data from 1) pooled BF samples, 2) previous DDA data from fractionated BF samples, and 3) published human DDA data, was used to extract abundance values for more than 2000 proteins from the SWATH data derived from each individual sample. An optimized normalization method was used prior to data processing. Using the integrated ion library, we found significant differences between burn severities, based on relative protein abundance. In addition, the biological processes relating to different burn depths were profiled through gene ontology enrichment analysis. Through this study, the quantitative profiling of burn blister fluid enabled identification of proteins related to burn severity and extent of injury. These will be further investigated as potential biomarkers to assist with clinical diagnosis of bun wound severity.