Fluorescence imaging techniques have been widely used to visualize biological molecules. Near-infrared BODIPYs are attractive candidates due to their intensive absorbance, fluorescence, photostability, and biocompatibility. Nevertheless, BODIPYs are highly hydrophobic, which is often problematic in fluorescence imaging of living cells. The uncharged nature of BODIPY molecules and their high hydrophobicity result in high affinity for lipid membranes, but this often leads to irreversible accumulation in subcellular membranes. In this paper, using three near-infrared aminostyryl-, hydroxystyryl- and pyrrolyl-BODIPYs 1-3 as an example, a simple method is proposed to solve the problem of high hydrophobicity and molecular aggregation by encapsulating luminophores in micelles of the amphiphilic block copolymer Pluronic® F127. The structural and optical characteristics of both NIR-BODIPYs 1-3 and their water-soluble forms NIR-BODIPY@Pluronic, as well as their effects on cell membrane permeability and fluorescence intensity in living cells, are analyzed in detail. HeLa cell staining tests demonstrate that all three types of nanoparticles with BODIPYs 1-3@Pluronic exhibit high membrane penetration and retention in cells, localizing in their cytoplasm. The nanoparticles with low dye loading are preferable for cell staining as they give the brightest images. Excellent optical properties, lack of toxicity, and high water solubility make the NIR-BODIPY@Pluronic nanoparticles as promising candidates for bioimaging in the red and NIR spectral ranges.