Mesoporous silicon nanoparticles loaded with salinomycin, a promising anticancer drug, were investigated as potential nanocontainers for cancer therapy. The drug loading and release were studied by means of the infrared spectroscopy, which revealed a gradual release of the drug with rate dependent on the mass ratio between the nanoparticles and salinomycin. In vitro studies revealed that the prepared nanoparticles loaded with salinomycin resulted in a notable cytotoxic effect on human glioblastoma cells, MCF-7 breast cancer cells and multidrug resistant MCF-7/MDR1 cells. In vivo experiments showed a strong suppression of the Lewis lung carcinoma tumor growth for 10–30 days after intraperitoneal administration of the nanocontainers. The obtained results indicate that salinomycin-loaded mesoporous silicon nanoparticles are prospective for mild chemotherapy of both primary cancer tumors and metastasis. The revealed efficiency against chemotherapy-resistant cancer stem cells and possibility of the intraperitoneal administration are very promising for further clinical applications of the prepared nanocontainers.