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Background Tuberous sclerosis is an autosomal dominant disorder with hamartomas in multiple organ systems. Facial angiofibromas (AF) are a common cutaneous manifestation of tuberous sclerosis. They may lead to significant cosmetic and psychological problems. Many treatment modalities have been used with variable satisfaction. Fractional photothermolysis (FP) is a novel concept of laser therapy, which induces non-contiguous microscopic thermal injury. Objective This study was designed to evaluate the efficacy and side effects of Nd:YAG laser treatment for facial AF by using spot-like irradiation technique similar to FP. Materials and methods Twelve patients (skin types III–IV, aged 17–45 years) with facial AF received monthly treatment with Nd:YAG laser in a pinpoint coagulation fashion. Clinical improvements were evaluated in five categories. Side effects were monitored at each follow-up visit. Results Excellent improvement was seen in 10 patients and good improvement in two at one month after the final treatment session. After 12 months of follow-up, no patient had significant recurrence of AF. Five patients were followed up for three years with few pinpoint-sized regrowth occurring; none of these patients received additional treatments. Side effects included transient erythema and edema in each patient but no bleeding, infection, dyspigmentation, or scarring. Conclusions The present study indicates that Nd:YAG laser is an effective and safe management for the fractional treatment of facial AF.