We aimed to study the antimicrobial and pro-healing potential of equine mesenchymal stromal cell secreted products (i.e. secretome), collected as conditioned media (mesenchymal stromal cell-conditioned media, MSC CM), in a novel in vivo model of methicillin-resistant Staphylococcus aureus (MRSA)-inoculated equine thorax wounds. Prospective in vivo study. Two Thoroughbred geldings. Six full-thickness cutaneous wounds were created bilaterally on the dorsal thorax of two horses (n = 12 wounds/horse). Wounds on the left thoraces were inoculated with MRSA on day 0. All wounds were then treated with either mupirocin ointment, MSC CM, or vehicle control (n = 4 wounds per group) once daily for 3 days. Photographs were taken to quantify wound scores and sizes, as well as samples to determine bacterial colony forming units (CFUs), at days 0, 1, 2, 3, 7, 14, 21, and 28. The wound edge was biopsied on days 0, 7, and 28, and scored histologically. Inoculated wounds had more bacterial CFUs at day 1 (p < .0001) and were larger in size at day 28 (p = .0009) than noninoculated wounds. Mupirocin-treated wounds were smaller than MSC CM and vehicle control-treated wounds at day 28 (p = .003). Mesenchymal stromal cell-conditioned media did not affect CFU numbers in inoculated and noninoculated wounds. Moreover, MSC CM did not affect the parameters of wound size or gross or microscopic wound scores over time. Mesenchymal stromal cell-conditioned media did not exhibit antimicrobial or pro-healing properties in the current study; however, the in vivo model of inoculated equine thorax wounds requires further optimization. This pilot study contributes to a growing understanding of the equine MSC secretome as an antimicrobial and pro-healing therapeutic for equine wounds.