A 27-year-old man who has sex with men presented with a painful lesion at the urethral meatus. A diagnosis of genital herpes was suspected, and initial tests for sexually transmitted infections (STIs), including syphilis serology, were negative. However, a polymerase chain reaction (PCR) swab for Treponema pallidum from the lesion was positive, and a diagnosis of chancre of primary syphilis at the meatus was made. Subsequently, the patient required urological surgery due to the formation of a urethral stricture. Chancre at the meatus and development of stricture are unusual complications of syphilis that may become more common in the future with increasing case numbers. We also discuss the development of PCR as a useful test for early primary syphilis.