We compared 3 months of eucaloric (12 kcal/kg/wk) steady state aerobic training (AER) to interval training (INT) in men at risk for insulin resistance. Primary outcomes included oral glucose tolerance testing (OGTT) and HOMA-IR 24 h and 72 h after each participants last exercise session. Secondary outcomes were VO 2max, anthropometry, and metabolic syndrome expressed as a summed z-score (zMS). We also performed a sub-analysis for participants entering the trial above and below the HOMA-IR study median. Mean (95% CI) AER (- 12.81 mg/dl; - 24.7, - 1.0) and INT (- 14.26 mg/dl; - 24.9, - 3.6) significantly improved 24 h OGTT. HOMA-IR did not improve for AER, but did for INT 24 h and 72 h post-exercise. VO 2max improved similarly for both groups. Changes in body mass for INT (- 2.29 kg; - 3.51, - 1.14), AER, (- 1.32 kg; - 2.62, 0.58)] and percent body fat [INT, - 0.83%; - 1.62, - 0.03), AER (- 0.17%; - 1.07, 0.06)] were only significant for INT. When examined as a full cohort, zMS improved for both groups. Upon HOMA-IR stratification, only high HOMA-IR AER showed significant improvements, while both low and high INT HOMA-IR participants demonstrated significant reductions (P<0.05). Eucaloric AER and INT appear to affect fasting glucose, OGTT and VO 2max similarly, while INT may have a greater impact on HOMA-IR and zMS.