The low absorption of biological substances and living tissues in the red/near-infrared region (therapeutic window) makes luminophores emitting in the range of ~650–1350 nm favorable for in vitro and in vivo imaging. In contrast to commonly used organic dyes, inorganic red/NIR emitters, including ruthenium complexes, quantum dots, lanthanide compounds, and octahedral cluster complexes of molybdenum and tungsten, not only exhibit excellent emission in the desired region but also possess additional functional properties, such as photosensitization of the singlet oxygen generation process, upconversion luminescence, photoactivated effects, and so on. However, despite their outstanding functional applicability, they share the same drawback—instability in aqueous media under physiological conditions, especially without additional modifications. One of the most effective and thus widely used types of modification is incorporation into silica, which is (1) easy to obtain, (2) biocompatible, and (3) non-toxic. In addition, the variety of morphological characteristics, along with simple surface modification, provides room for creativity in the development of various multifunctional diagnostic/therapeutic platforms. In this review, we have highlighted biomedical applications of silica-based materials containing red/NIR-emitting compounds.