Background: Numerous people suffer from diabetes mellitus (DM) and resultant diabetic foot ulcers (DFU), which lack effective treatment. Photobiomodulation (PBM) has accelerated wound healing in diabetic animals and patients in some studies. However, there is scant information on the number and activation state of skin mast cells (MCs) in PBM-treated diabetic wounds. Objective: We intend to assess the influence of the number of MCs and degranulation in the remodeling step of an infected wound model on wound strength and its microbial flora in a type 1 DM (T1DM) rat model by administration of PBM, condition medium (CM) derived from human bone marrow mesenchymal stem cells (hBMMSCs), and the combination of PBM+CM. Methods: We prepared CM by culturing hBMMSCs. T1DM was induced in 72 rats and, after 1 month, we created one excisional wound in each rat. All wounds were infected with methicillin-resistant Staphylococcus aureus (MRSA). We divided the rats into four groups: (n = 18): (i) control; (ii) PBM; (iii) CM, and (iv) PBM+CM. On days 4, 7, and 15, we conducted microbiological, tensiometrical, and stereological analyses. The type of MCs (T1MCs, T2MCs, or T3MCs) and total number of MCs (TOMCs) were counted by light microscopy. Results: On day 15, the PBM+CM, PBM, and CM groups had significantly increased wound strength compared with the control group. There was a significant decrease in colony-forming units (CFU) at all time points in the PBM+CM and PBM groups. The PBM+CM and PBM groups had more stable MCs (T1MCs), less significant degranulated MCs (T2MCs), less significant disintegrated MCs (T3MCs), and less significant TOMCs compared with the control group at all time points. Conclusions: PBM+CM and PBM treatments significantly increased the healing process in an ischemic and MRSA-infected wound model of T1DM rats. PBM+CM and PBM significantly decreased both TOMCs and their degranulation, and significantly decreased CFU.