An 18-year-old man was seen at a Sexually Transmitted Infections (STIs) clinic for counselling and treatment of Chlamydia trachomatis genital infection which had been diagnosed during a screening survey of high-school students. For two months he had reported conjunctival hyperaemia, increased tearing, itching, and mucopurulent secretions, predominantly on the left eye. His ophthalmologist had made a diagnosis of follicular conjunctivitis and lower superficial punctate keratitis (left eye > right eye), irresponsive to topical treatment. Chlamydial conjunctivitis was suspected and confirmed by a positive nucleic acid amplification test (NAAT) performed on conjunctival scraping. The patient was treated with azithromycin 1 g single dose orally and tetracycline/ betamethasone eye ointment for one month. A complete resolution of symptoms was observed three months after aetiological treatment. This case highlights the need to include C. trachomatis infection in the differential diagnosis of acute or chronic follicular conjunctivitis among sexually active young individuals.