Hypoandrogenemia, a frequent finding in men with obesity, is defined by low concentrations of serum testosterone. Although immunoassay (IA) is the most used method for the determination of this steroid in clinical practice, liquid chromatography-mass spectrometry (LC-MS/MS) is considered a more reliable method. In this study, we aimed to compare IA versus LC-MS/MS measurement for the diagnosis of hypoandrogenemia in a cohort of 273 nondiabetic young obese men. Mean total testosterone (TT) levels were 3.20 ± 1.24 ng/mL for IA and 3.78 ± 1.4 ng/mL for LC-MS/MS. 53.7% and 26.3% of patients were classified as presenting hypoandrogenemia with IA and LC-MS/MS, respectively. Considering LC-MS/MS as the reference method, sensitivity and specificity of IA were 91.4% (95% CI 82.3–96.8) and 61.1% (95% CI 54.0–67.8), respectively. IA presented an AUC of 0.879 (95% CI 0.83–0.928). Multivariate regression analysis indicated that sex hormone-binding globulin (SHBG) concentrations (p = 0.002) and insulin resistance (p = 0.008) were factors associated with discrepant IA values. In conclusion, the determination of TT by IA in nondiabetic young men with obesity yields lower concentrations of TT than LC-MS/MS, resulting in an equivocal increased diagnosis of hypoandrogenemia, which could lead to inaccurate diagnosis and unnecessary treatment.