Breast cancer is now one of the leading causes of death in women worldwide. Finding a cure is, therefore, critical for women’s health. Marine sponge-derived drugs have gained interest in breast cancer treatment. The development of marine natural products into cancer therapy includes several stages. It starts with the screening using the cytotoxic test method, a preclinical trial using the animal mode, and clinical trial phases I and II. In this study, we focus on the basic cytotoxic test to find the new source of anti-breast cancer compounds derived from Agelas nakamurai to know the potential for further investigation to become lead compounds. However, the anti-breast cancer potential of the Indonesian marine sponge A. nakamurai has never been studied. This study aimed to evaluate the anti-breast cancer potential of extract and fraction of A. nakamurai against epithelial human breast cancer cells (MDA-MB-231 and MCF-7 cells line) and to preliminary profile the known active compounds. The maceration using methanol was used for extraction and followed by partitioning with varied solvents [ethyl acetate (EtOAc), butanol, and water]. Fractionation was done using normal phase open column chromatography, and liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) was used for analyzing compounds. MDA-MB-231, MCF-7, and HEK-293 cell lines were used for biological activities. The chromatographic separation of the EtOAc fraction led to the F7 subfraction which strongly inhibits proliferation against the MDA-MD-231 (IC50: 10.677 μg/mL), MCF-7 (IC50: 15.154 μg/mL), and HEK-293 cells line. The LC-MS/MS data of active fraction F7 contained gelatin-D and ageloxime-D. This study reported that fraction 7 of A. nakamurai showed strong activity against MDA-MB-231, MCF-7, and HEK-293 cell lines. Further analysis will be carried out to know the mechanisms of action of active compounds.