Background This pilot study examined long-term pulse wave velocity (PWV) and peak oxygen uptake (VO2peak) outcomes following a 12-week moderate-intensity aerobic or resistance training programme in kidney transplant recipients. Method Single-blind, bi-centre randomised controlled parallel trial. 42 out of 60 participants completed a 9-month follow-up assessment (Aerobic training = 12, Resistance training = 10 and usual care = 20). Participants completed 12 weeks of twice-weekly supervised aerobic or resistance training. Following the 12-week exercise intervention, participants were transitioned to self-managed community exercise activity using motivational interviewing techniques. Usual care participants received usual encouragement for physical activity during routine clinical appointments in the transplant clinic. PWV, VO2peak, blood pressure and body weight were assessed at 12 weeks and 12 months, and compared to baseline. Results ANCOVA analysis, covarying for baseline values, age, and length of time on dialysis pretransplantation, revealed a significant mean between-group difference in PWV of -1.30 m/ sec (95%CI -2.44 to -0.17, p = 0.03) between resistance training and usual care groups. When comparing the aerobic training and usual care groups at 9-month follow-up, there was a mean difference of -1.05 m/sec (95%CI -2.11 to 0.017, p = 0.05). A significant mean between-group difference in relative VO2peak values of 2.2 ml/kg/min (95% CI 0.37 to 4.03, p = 0.02) when comparing aerobic training with usual care was revealed. There was no significant between group differences in body weight or blood pressure. There were no significant adverse effects associated with the interventions. Conclusions Significant between-group differences in 9-month follow-up PWV existed when comparing resistance exercise intervention with usual care. A long-term between-group difference in VO2peak was only evident when comparing aerobic intervention with usual care. This pilot study, with a small sample size, did not aim to elucidate mechanistic mediators related to the exercise interventions. It is however suggested that a motivational interviewing approach, combined with appropriate transition to community training programmes, could maintain the improvements gained from the 12-week exercise interventions and further research in this area is therefore warranted. © 2017 O'Connor et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.