Objective To compare the clinical efficacy and safety of domestic and imported fluconazole injections in treating patients with deep fungal infections. Methods A prospective multicentre study in 170 cases of deep fungal infections was performed. Results There were no statistically significant differences in recovery rates (50.9%v 50.9%), effective rates (83.6%v 89.1%), clearance rates of fungals (83.9%v 89.1%), and side-effect rates (8.9%v 9.1%) between test group and control group. Conclusion Both domestic and imported fluconazole injections are safe and effective drugs for treating deep fungal infections.