Basal stem rot disease in pepper caused by P. capsici is the ultimate disease which can lead to the death of the plant. Trichoderma sp. produces secondary metabolite which is effective for controlling this disease. To know the effectiveness of Trichoderma sp. secondary metabolite, the experiment with different concentrations placed in the polybag to control basal stem rot disease in pepper was conducted from March to June 2020 at UPTD Pengembangan Perlindungan Tanaman Perkebunan (P2TP), Plantation Office, East Borneo. A completely randomized design with five treatments and ten replications was applied in this experiment. The data were analyzed using analysis of variance. If there is a significant difference, the test will continue at the least significant difference of 5%. The study entitled “The Growth of Pepper Seeds Attacked by Basal Stem Rot Disease (Phytophthora capsici) on Application of Trichoderma sp. Secondary Metabolite” concluded three main points. First, based on the intensity of disease attack, the average of both shoot internode number and shoot internode length of Trichoderma sp. secondary metabolite was mostly effective to control the disease attack or at MS20 concentration namely 88.06% of the intensity of disease attack. Second, based on the average number of leaves, MS5 concentration was able to control the disease progression by calculating the number of grown leaves, around 75.40 leaves. Last, based on the growth of the plant, the effective use of secondary metabolite was at MS10 concentration with the height of the plant 71.50 cm.