Intense pulsed light (IPL) has shown diverse results in hair clearance related to treatment protocols or skin phototype. Hirsutism may be due to endocrine disease, as in polycystic ovary syndrome (PCOS) and congenital adrenal hyperplasia (CAH), both of which conditions may be associated with obesity. Obesity complicates the metabolic pattern, particularly in terms of insulin resistance, which may worsen the clinical condition of hirsutism. This study evaluated the role of obesity in photoepilation, comparing the clinical efficacy, long-term hair reduction and patient satisfaction in 40 hirsute women with PCOS or CAH, either obese (n = 20) or of normal weight (n = 20). The IPL settings were the same for both groups, but the number of sessions varied according to the clinical results. Obese patients showed a statistically significant severity of initial hirsutism if compared to the non-obese population and, for this reason, required more sessions to achieve hair reduction. The results were maintained at the 2-year follow-up examination, with a high satisfaction rate in both groups.