Background <p>Oral mucositis (OM) is a debilitating treatment-related complication that affects most children undergoing chemotherapy. This dual-arm clinical trial aimed to evaluate the efficacy of photobiomodulation (PBM) for prevention and photodynamic therapy (PDT) using indocyanine green (ICG) and low-level laser for treating methotrexate (MTX)-induced OM in pediatric patients with hematologic cancers.</p> Methods <p>In the prevention arm, patients were initially assigned to a control group (received no laser) and subsequently reassigned to a PBM group in their next cycle, allowing intra-patient comparison under similar chemotherapy protocols. In the treatment arm, patients diagnosed with OM were randomly assigned to either a control group (sham laser) or a PDT group.</p> Results <p>In the prevention arm, PBM led to a significant reduction in the incidence of OM from 66.67% to 6.67% (<i>p</i> &lt; 0.05). In the treatment arm, the PDT group showed a significant reduction in the scores of all scales (WHO, NCI, and WCCNR) at both 3 days and 5 days after starting the treatment compared to the control group (<i>p</i> &lt; 0.05). Moreover, the reduction in the NCI score from the third to the fifth days after the starting treatment is higher in the PDT group compared to the control group (<i>p</i> &lt; 0.05).</p> Conclusion <p>PBM appears to be a safe and effective approach for the prevention of MTX-induced OM in pediatric patients with hematologic cancers. Additionally, PDT using ICG and a low-level laser demonstrates promising results in treating OM lesions. Therefore, these findings highlight the efficacy of PBM for managing MTX-induced OM in this patient group.</p> Trial registration <p>The study has been registered on irct.behdasht.gov.ir on 4 December 2022 (Trial Registration Number: IRCT20120101008585N16).</p>