Purpose Eccentric exercise has been proposed as an alternate modality for chronic disease patients who cannot tolerate strenuous or vigorous intensity exercise. However, there is limited information regarding the biological benefits of this type of training compared to 'traditional' exercise. In this exploratory randomised clinical trial, we evaluated the feasibility and efficacy of eccentric exercise in the amelioration of markers of insulin resistance and inflammation. Methods Ten participants (age 50.0 ± 15 years, BMI 31.3 ± 7.1 kg/m2) with newly diagnosed T2DM and a sedentary lifestyle were randomly assigned to eccentric or concentric training performed during ten 30-min sessions of aerobic exercise over a 2-week period. Fasting blood samples were obtained pre- and 24 h post-intervention to determine insulin resistance (HOMA-IR, OGTT) and circulating cytokine (IL-6, TNF-a) concentrations. Results Despite the reduced heart rate (p = 0.008), the eccentric training group performed more work over the ten training sessions (p = 0.016) with no differences in the participant's perceived exertion (p = 0.69). No significant between- or within-group changes were observed for OGTT, HOMA-IR or markers of inflammation (p > 0.05). However, there was a modest but consistent amelioration of OGTT, IL-6 and TNF-a that was been observed in the eccentric training group but not in the concentric training group. Conclusion Preliminary findings from this exploratory study would tend to suggest that short-term eccentric exercise is well tolerated in previously sedentary T2DM patients and that the trend towards reductions in circulating insulin resistance and inflammatory markers requires validation in an adequately powered clinical trial conducted over a longer duration.