Cancer, the second-leading cause of death worldwide after cardiovascular diseases, is a deadly disease caused by numerous mutations that affect cell growth and differentiation. While there is no definitive cure for cancer yet, new target molecules are being identified with the help of developing technology, and appropriate treatment protocols are being developed. Since both normal and malignant cells are exposed to cytotoxic effects in traditional treatment methods, the development of less-side-effect and targeted treatment methods has become important. With the development of nanotechnology, the development of various nanodrug delivery systems (DDSs) has been targeted. In our study, we investigated the antiproliferative and antimicrobial activities of rutin-modified carbon nanofiber (ACNFr)-based aerogels loaded with krill oil (KO) (ACNFr-KO). Our results showed that ACNFr-KO aerogels were observed to have a significant anti-proliferative effect on the human breast cancer cell line MCF-7. In addition to this, ACNFr-KO aerogels were found to have antimicrobial activity against the gram-positive bacterium E. faecalis ATCC 29212. The results of our study suggest that rutin-modified CNF-based aerogels loaded with KO, which act as a DDS, have the potential to enhance targeted drug delivery and improve therapeutic outcomes in biomedical applications.