Febrile seizure is the most common neurological disorder in children and occurs in 2 to 5% of them. The possibility of febrile seizure recurrence induces a grave concern to parents. Prophylactic benzodiazepines are usually used to prevent the recurrence. However, previous studies showed no difference between the preventive effect of clobazam and diazepam. Thus, this study aimed to compare the effects of clobazam and diazepam in preventing febrile seizure recurrence in children. A double blind, randomized, controlled trial was conducted on 160 children from six months to 5 years of age with febrile seizure. Patients were matched for age, sex, underlying diseases and risk factors for recurrence and randomly assigned to two groups to receive either 0.33 mg/kg of oral diazepam, every 8 h for two days, or 1 mg/kg of oral clobazam every 12 h for 2 days. All patients were followed-up for the frequency and time of febrile seizure recurrence, and drug side effects for 12 months. Descriptive statistics were calculated and chi-square and t- tests were used to compare the two groups. The mean age of the children in the diazepam and clobazam groups were 29.61 ± 13.1 and 29.7 ± 11.5 months, respectively (P = 0.755). In clobazam group, the frequencies of febrile seizure recurrence were 10%, 5% and 5% at 3, 6 and 12 months after the first attack. At the same time, the frequencies of the recurrence in the diazepam group were 23.8%, 17.5% and 15%, respectively (p < 0.05). The two groups were not significantly different in terms of the drug side effects (p = 0.194). The group treated with clobazam experienced less febrile seizure recurrence in the 12 months follow-up. Thus, clobazam can be used as an effective medication to prevent febrile seizure recurrence in children.