To develop an efficient method for large preparation of javanicin from Fusarium solani, a rapid and simple method by high-speed countercurrent chromatography was established based on average polarity (P' values) and partition coefficients (K values) of crude samples. A suitable solvent system for high-speed countercurrent chromatography was selected from many possible biphasic solvent systems. HSCCC was successfully applied to separate and purify javanicin, the main bioactive component of solid cultures of the fungus F. solani isolated from the fruiting body of Trametes trogii, with petroleum ether-ethyl acetate-methanol-water (4:3:2:1, v/v) as solvent system. A total amount of 40.6 mg of javanicin was obtained from 100 mg crude sample. The purity of javanicin was 92.2% with a recovery of 95.1%, as determined by high-performance liquid chromatrography. The molecular structure was identified primarily by NMR and MS methods. The results indicated that high-speed countercurrent chromatography could be a powerful technology for separating naphthoquinones from the solid cultures of the fungus F. solani. It is also of significance that the separation of javanicin from natural source was carried out for the first time utilizing high-speed countercurrent chromatography.