The aim of the study was to observe the effectiveness of a photo-biomodulation (PBM) protocol for the prevention of oral mucositis (OM) in patients undergoing allogeneic hematopoietic stem cell transplantation (aHSCT). A case-control study was conducted on 40 patients undergoing aHSCT. The patients were divided into two groups; the preventive group (PG) included 20 patients (7 females and 13 males) who were subjected to intra-oral PBM for five sessions a week, starting one day before the conditioning regimen and continuing until the 10th day after transplantation (D+10). In each session, ten points on the at-risk mucosal surfaces were irradiated using a double diode laser that emits two wavelengths simultaneously at 650 nm and at 904–910 nm with the following parameters at each point: energy of 4 J, and power of 88.9 mW. The control group (CG) included 20 patients (10 females and 10 males) who were not subjected to laser therapy and were selected retrospectively to compare the obtained results. For all patients, OM was assessed by the World Health Organization (WHO) grading scale. Eight patients in the PG did not experience OM during their hospitalization period (with grade 0). Severe OM was observed in 40% of the patients in the PG, while in the CG, severe OM was shown in 85% of the patients. The mean duration of OM in the PG was significantly lower than that of CG (4.7 days in the PG and 15 days in the CG) (p < 0.001). The study demonstrated that the preventive PBM protocol reduced the severity and duration of OM in patients undergoing aHSCT.