Introduction Gonorrhea is a major sexually transmitted infection (STI) globally with increasing trends. Despite limited data, gonorrhea remains an important public health problem in Bhutan. Methods A descriptive study was carried out in two Bhutanese hospitals; Jigme Dorji Wangchuck National Referral Hospital and Phuentsholing General Hospital in 2015. Patients suspected of gonococcal urethritis were sampled, treated and followed up at two weeks. Gonococcal isolates were identified and tested for antibiotic susceptibility by the Calibrated Dichotomous Sensitivity Test (CDS) method. Results Of the 524 patients, 2.3% (12) were females. Most (46.6%) patients belonged to the 26-35 years age group. About 58% were lost to follow up; 62% (277) of males and all (12) females. N. gonorrhoea was positive in 76% (398) of microscopy and 73.1% (383) by culture. Resistance against ciprofloxacin, penicillin, tetracycline and nalidixic acid were 85.1%, 99.2%, 84.8% and 99.7% respectively. Nearly all the isolates were sensitive to cefpodoxime, ceftriaxone and azithromycin. Sixty-seven percent (350) were treated with injection ceftriaxone alone, 32% (169) with ceftriaxone and oral doxycycline and 1% (5) with ceftriaxone, doxycycline and metronidazole. Probable treatment failure was seen only in one patient (0.5%). Conclusions Gonococcal resistance to currently used antibiotics was low and there was a high clinical cure rate. Compliance to treatment guidelines need reinforcement addressing antibiotic regimen, tracing sexual partners and addressing the social stigma. National STI programs should be more women-friendly for effective management, prevention and control of STIs. Laboratories must adopt more reliable susceptibility testing methods, the Minimum Inhibition Concentration method.