Multi-drug resistance of pathogenic microorganisms is a serious threat to human health, especially Candida albicans, the most common opportunistic clinical fungal pathogen causing systemic infections with high mortality. Widespread and repeated use of azoles has led to rapid antifungal drug resistance, highlighting the need for new therapeutic strategies such as synergistic drugs. A high-throughput synergy screening (HTSS) method was developed to identify microbial natural products that synergize with low-dose ketoconazole (KTC) against fungal pathogens. Screening of a microbial natural product library from endophytic bacteria associated with traditional Chinese medicine Alisma orientale led to the identification of an extract from endophytic actinomycete Streptomyces sp. CNS-42 with synergistic antifungal activity. Bioassay-directed fractionation of a large-scale (42 L) culture of CNS-42 yielded four known indolecarbazoles (1–4). Compounds 1 (N-formyl-staurosporine) and 2 (N-acetyl-staurosporine) showed potent synergistic antifungal activities with MIC values of 6.25 and 0.78 μg ml⁻¹, respectively, when combined with 25% of the MIC of KTC against C. albicans, but weak or no antifungal activity (MIC ≥ 100 μg ml⁻¹) when tested singly. This study reports the new synergistic antifungal activity of indolecarbazoles, providing a basis for their further pharmaceutical application.