Aim Physical activity is a potent way to impede vascular ageing. However, patients who suffer from peripheral artery disease (PAD) are often unable to exercise adequately. For those patients, we have developed individual shear rate therapy (ISRT), which is an adaptation of external counterpulsation and enhances endovascular fluid shear stress to increase collateral growth (arteriogenesis). To evaluate the effects of physical exercise and ISRT on the telomere biology of peripheral blood mononuclear cells (PBMCs), we conducted two clinical trials. Methods In the ISRT‐1 study, we assessed PBMC telomerase activity in 26 young healthy volunteers upon a single (short‐term) ISRT session and a single treadmill running session. In the ISRT‐2 study, we investigated PBMC telomere biology of 14 elderly patients with PAD, who underwent 30 h of (long‐term) ISRT within a 5‐week period. Results We demonstrate that telomerase activity significantly increased from 39.84 Total Product Generated (TPG) Units ± 6.15 to 58.10 TPG ± 10.46 upon a single treadmill running session in healthy volunteers. In the ISRT‐2 trial, PBMC telomerase activity and the mRNA expression of the telomere‐protective factor TRF2 increased from 40.87 TPG ± 4.45 to 60.98 TPG ± 6.83 and 2.10‐fold ± 0.40, respectively, upon long‐term ISRT in elderly patients with PAD. Conclusion In summary, we show that acute exercise and long‐term ISRT positively affect PBMC telomerase activity, which is indicative for an improved regenerative potential of immune cells and vascular tissues. Long‐term ISRT also enhances the gene expression of the telomere‐protective factor TRF2.