To explore the safety and feasibility of low fluence intense pulsed light (IPL) for treating pediatric patients with moderate-to-severe blepharitis and to analyze potential factors associated with the recovery of meibomian glands (MG) dropout, a retrospective, noncomparative study, including 17 blepharitis patients (33 eyes) aged between 5 and 16 years old was conducted. All of the participants were given 4 continuous sessions of low-fluence (9−12 J/cm2) IPL at 3−4 week intervals. Corneal fluorescein staining (CFS), tear breakup time (BUT), inferior tear meniscus height, Demodex presence, and MG morphology were examined before and after the treatment. Results indicated that CFS, BUT and MG morphology (central/total gland area ratio and gland signal index) had significantly improved (p < 0.05). Symptoms and signs such as severe corneal neovascularization, limbal pannus and conjunctival congestion also subsided. Among age, gender, presence of Demodex and interval before diagnosis, age initiating the formal treatment was confirmed as a negatively correlated factor of the recovery of MG dropout (p = 0.032, B = −1.755). No notable adverse events were reported. In conclusion, low fluence IPL seems to be a safe and effective alternative for moderate-to-severe pediatric blepharitis, and MG dropout is prone to recover in younger patients.