Lifestyle measures (LSM) should be the first line approach offered for obesity related functional hypogonadism (FH). When LSM fail, a role of testosterone replacement treatment (TRT) is unclear. GLP1 receptor agonist liraglutide is linked to progressive and sustained weight loss. A potential direct impact of GLP1 on hypothalamus-pituitary-testicular (HPT) axis was reported in animal models. We aimed to compare the effects of liraglutide and TRT on FH in obese men that had been poor responders to LSM, by means of reversal of FH and weight reduction. We designed 16-week prospective randomized open-label study with 30 men (aged 46.5±10.9 years, BMI 41.2±8.4 kg/m2, mean ± SD) that were randomized to liraglutide 3.0 mg QD (LIRA) or 50 mg of 1% transdermal gel QD (TRT). Sexual function and anthropometric measures were assessed. A fasting blood was drawn for determination of endocrine and metabolic parameters followed by OGTT. Model-derived parameters including HOMAIR and calculated free testosterone (cFT) were calculated. Total testosterone significantly increased in both arms (+5.9±7.2 in TRT vs +2.6±3.5 nmol/l in LIRA) and led to improved sexual function. LIRA resulted in a significant increase of LH and FSH (p<0.001 for between treatment effect). Subjects treated with LIRA lost on average 7.9±3.8 kg compared with a 0.9±4.5 kg loss in TRT (P<0.001). Metabolic syndrome was resolved in two patients in LIRA and in no subjects in TRT. Liraglutide was superior to TRT in improving an overall health benefit in men with obesity associated FH after LSM failed.