Ankle brachial index (ABI) is a diagnostic tool for peripheral artery disease (PAD), which is an important issue in hemodialysis (HD) patients. We enrolled 198 maintenance HD patients in this study. PAD is defined as ABI ≤ 0.90. Only PAD patients received far-infrared (FIR) therapy using the WS TY101 FIR emitter for 40 min during each HD session, three times weekly for 6 months. The ABI was measured at the bilateral lower extremities for 4 times [pre-dialytic timing (0 min) and 40 min after the initiation of HD session at both day 0 and 6 months after the FIR therapy]. The primary outcome is the change in ABI. There were 51 out of 198 patients with PAD. In comparison with the period without FIR therapy in the 51 PAD patients, 6 months of FIR therapy significantly improved the ABI of the right/left side for 0 min (from 0.77 ± 0.19 to 0.81 ± 0.20, p = 0.027/0.79 ± 0.20 to 0.81 ± 0.17, p = 0.049), 40 min during HD (from 0.73 ± 0.23 to 0.83 ± 0.19, p < 0.001/from 0.77 ± 0.21 to 0.83 ± 0.18, p < 0.001), and the incremental change between 0 and 40 min (from − 0.04 ± 0.14 to 0.05 ± 0.13, p = 0.007/from − 0.05 ± 0.13 to 0.03 ± 0.11, p = 0.012), respectively. In conclusion, the application of FIR therapy for 40 min, three times weekly for 6 months, has improved the ABI of both lower extremities, thus providing a new strategy of PAD treatment in HD patients.