Purpose To identify the incidence of methicillin-resistant Staphylococcus aureus (MRSA) in Indigenous compared to non-Indigenous children with skin and soft tissue infections (SSTIs). Methodology Following ethical approval, electronic hospital records were retrospectively reviewed to identify microbiological swabs from patients who underwent incision and drainage of SSTIs at Townsville University Hospital between January 2020 and December 2024. Patients under 16 years with their ethnicity data were included. Results 480 children met the inclusion criteria. 243 (51%) identified as Indigenous and 237 (49%) non-Indigenous. MRSA was isolated in significantly more Indigenous (40%, 98/243) than non-Indigenous (19.4%, 46/237) patients (P < 0.001). Indigenous children were 2.8 times more likely to have MRSA (OR: 2.8, 95% CI: 1.99, 3.96). Staphylococcus aureus was cultured in 38.3% (184 / 480) of samples. Other cultured organisms included Streptococcus species (11.6%), mixed skin flora (5.6%) and mixed enteric and anaerobic Bacteria (4.3%). Other multi-resistant organisms included Extended Spectrum Beta-Lactamase producing E. coli (2/480) and Mycobacterium Abscesses (1/480). SSTIs most commonly affected the limbs (28.3%) followed by head and neck (22%), buttocks (14.5%), torso (9.6%), perianal / perineal (9.6%) and groin (5.6%). Most SSTIs were drained by the paediatric surgeons (67%), followed by Orthopaedics (17.5%), with smaller numbers by maxillofacial, ear-nose and throat, and general surgery. Conclusions We identified higher rates of MRSA in Indigenous children with SSTIs compared to non-Indigenous children, justifying empiric MRSA antimicrobial coverage for Indigenous children. Future prospective studies should include follow-up to assess rates of recurrence, side effects of antibiotics and whether the same trend continues into adulthood.