<b><i>Introduction:</i></b> Gonococcal infection of the penile raphe is rarely encountered in the clinical setting. The study aimed to understand the incidence, sites, clinical manifestations, and treatment of gonococcal infection of the penile raphe. <b><i>Methods:</i></b> We enrolled men with gonococcal infection of the penile raphe and men with urethral gonorrhea from January 2010 to December 2021. All patients’ demographic data and clinical characteristics were recorded. All patients were treated with ceftriaxone. Incision and drainage were performed in patients with non-ruptured abscesses. Nodules and sinus tract-like lesions that did not resolve after 1 month of treatment were excised. <b><i>Results:</i></b> Among 2,736 men who presented with urethral gonorrhea from January 2010 to December 2021, 5 (0.18%) had accompanying gonococcal infection of the penile raphe. An additional two men presented with gonococcal infection of the penile raphe without urethritis. Thus, 7 (0.26%; confidence interval, 0.11–0.56%) of 2,738 men had urethral gonorrhea or gonococcal infection of the penile raphe confirmed both clinically and by laboratory testing. Lesions were present in the frenulum of the prepuce and at the median aspect, proximal end, distal end, and both the proximal and distal ends of the penile raphe. The lesions manifested as abscesses, ulcers, a nodule, and a nodule with a sinus-like lesion. All lesions exhibited tenderness. All seven patients were cured after treatment. <b><i>Conclusion:</i></b> Gonococcal infection of the penile raphe is a rare, atypical type of involvement of the male urogenital tract by <i>Neisseria gonorrhoeae</i>. It may be a local complication of urethral gonorrhea or an independent primary infection. The proximal end, distal end, and median aspect of the penile raphe can be infected by <i>N. gonorrhoeae</i>. Cutaneous lesions present as abscesses, ulcers, nodules, and sinus-like lesions. Ceftriaxone is effective, but sinus-like lesions require surgery.