Aim: This study aimed to assess the feasibility and safety of administering cyclosporin A (CsA) as a 2-hour, twice-daily intravenous infusion versus continuous 24-hour infusion in allogeneic hematopoietic stem cell transplant (HSCT) patients. Methods: A prospective randomized study was conducted, dividing adult HSCT patients into two groups based on the CsA administration method. The primary outcomes assessed the incidence of acute graft-versus-host disease (aGVHD) and CsA-related adverse events. Secondary outcomes included the correlation between time concentrations and area under concentration-time curves (AUCs) and performing a cost-effectiveness analysis. Results: 31 allogeneic HSCT patients were enrolled, with 38.7% initially diagnosed with acute myeloid leukemia (AML). There was no significant difference between the two study groups in developing aGVHD, distribution of different aGVHD types, transplantation outcomes, and mortality. The obtained AUCs showed no significant difference between the two infusion methods at all time points. Regarding the cost-effectiveness, the 2-hour infusion group had a higher total of quality-adjusted life-years (QALYs) per patient (1.77) and lower total costs per patient (3802.15 USD) compared to the 24-hour infusion group (QALYs: 0.74, costs: 13239.22 USD). The incremental cost-effectiveness ratio (ICER) for the intervention group was -9158.53. Conclusion: Administering CsA as a 2-hour twice-daily infusion is both feasible and safe for allogeneic HSCT patients. The study demonstrates that the 2-hour infusion regimen is non-inferior to the conventional 24-hour infusion in terms of aGVHD incidence and adverse events. Moreover, 2-hour infusion strategy proves to be more cost-effective. Further research is necessary to validate these findings and guide clinical practice.