Recently, various attempts have been made to apply diverse types of nanoparticles in biotechnology. Silica nanoparticles (SNPs) have been highlighted and studied for their selective accumulation in diseased parts, strong physical and chemical stability, and low cytotoxicity. SNPs, in particular, are very suitable for use in drug delivery and bioimaging, and have been sought as a treatment for ischemic diseases. In addition, mesoporous silica nanoparticles have been confirmed to efficiently deliver various types of drugs owing to their porous structure. Moreover, there have been innovative attempts to treat ischemic diseases using SNPs, which utilize the effects of Si ions on cells to improve cell viability, migration enhancement, and phenotype modulation. Recently, external stimulus-responsive treatments that control the movement of magnetic SNPs using external magnetic fields have been studied. This review addresses several original attempts to treat ischemic diseases using SNPs, including particle synthesis methods, and presents perspectives on future research directions.