Metformin, a drug widely used to treat insulin resistance, and training that combines aerobic and strength exercise modalities (i.e., concurrent training) may improve insulin sensitivity. However, there is a paucity of clinical trials investigating the effects of concurrent training, particularly on insulin resistance and fat oxidation in overweight and obese patients. Furthermore, only a few studies have compared the effects of concurrent training with metformin treatment. Therefore, the aim of this study was to examine the effects of a 12-week concurrent training program versus pharmaceutical treatment with metformin on maximum fat oxidation, glucose metabolism, and insulin resistance in overweight or obese adult patients. Male and female patients with insulin resistance were allocated by convenience to a concurrent training group (n = 7 (2 males); age = 32.9 ± 8.3 years; body mass index = 30 ± 4.0 kg·m−2) or a metformin group (n = 7 (2 males); age = 34.4 ± 14.0 years; body mass index = 34.4 ± 6.0 kg·m−2). Before and after the interventions, all participants were assessed for total body mass, body mass index, fat mass, fat-free mass, maximum oxygen consumption, maximal fat oxidization during exercise, fasting glucose, and insulin resistance through the homeostatic model assessment (HOMA-IR). Due to non-normal distribution of the variable maximal fat oxidation, the Mann–Whitney U test was applied and revealed better maximal fat oxidization (Δ = 308%) in the exercise compared with the metformin group (Δ = −30.3%; p = 0.035). All other outcome variables were normally distributed, and significant group-by-time interactions were found for HOMA-IR (p < 0.001, Δ = −84.5%), fasting insulin (p < 0.001, Δ = −84.6%), and increased maximum oxygen consumption (p = 0.046, Δ = 12.3%) in favor of the exercise group. Similar changes were found in both groups for the remaining dependent variables. Concurrent training seems to be more effective compared with pharmaceutical metformin treatment to improve insulin resistance and fat oxidation in overweight and obese adult patients with insulin resistance. The rather small sample size calls for more research in this area.