Metronidazole is recommended as the first-line treatment for Bacterial Vaginosis (BV). With respect to various side effects of metronidazole and increased antibiotic resistance, it seems necessary to find a medication with fewer side effects. The present study aimed to compare the effects of Mycocin vaginal cream (made of garlic and thyme) and metronidazole vaginal gel on treatment of the patients with BV. This clinical trial which was conducted on 120 married women aged 18-44 years whose infection with BV was diagnosed through clinical Amsel criteria. The participants were randomly divided into two groups of 60 receiving Mycocin vaginal cream or metronidazole vaginal gel for seven days. Clinical Amsel criteria and the patients’ complaints were assessed again 7 days after completion of the treatment period. The results showed a decrease in the patients’ complaints and clinical Amsel criteria after the treatment with Mycocin vaginal cream and metronidazole vaginal gel. However, no significant difference was observed between the two groups regarding clinical improvement in Amsel criteria (P<0.05). Mixed Garlic and Thyme vaginal cream (Mycocin) seems to be an appropriate alternative for metronidazole vaginal gel in treatment of BV.